From fae9a89dca149936333a1b7e86b28deee474537a Mon Sep 17 00:00:00 2001 From: Junpeng Zhang Date: Sun, 4 Feb 2024 22:43:27 +0800 Subject: [PATCH 1/3] Delete man/Module_group_sim.Rd --- man/Module_group_sim.Rd | 39 --------------------------------------- 1 file changed, 39 deletions(-) delete mode 100644 man/Module_group_sim.Rd diff --git a/man/Module_group_sim.Rd b/man/Module_group_sim.Rd deleted file mode 100644 index c988f19..0000000 --- a/man/Module_group_sim.Rd +++ /dev/null @@ -1,39 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_group_sim} -\alias{module_group_sim} -\title{module_group_sim} -\usage{ -module_group_sim(Module.group1, Module.group2, sim.method = "Simpson") -} -\arguments{ -\item{Module.group1}{List object, the first list of module group.} - -\item{Module.group2}{List object, the second list of module group.} - -\item{sim.method}{Methods for calculating similatiry between two modules, select one of three methods (Simpson, Jaccard and Lin). Default method is Simpson.} -} -\value{ -Similarity between two list of module groups -} -\description{ -Calculating similarity between two list of module groups -} -\examples{ -library(GSEABase) -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) -modulegenes_igraph <- module_igraph (ceRExp, mRExp) -Sim <- module_group_sim(geneIds(modulegenes_WGCNA), geneIds(modulegenes_igraph)) - -} -\references{ -Simpson E H. Measurement of diversity. Nature, 1949, 163(4148): 688-688. - -Jaccard P. The distribution of the flora in the alpine zone. 1. New phytologist, 1912, 11(2): 37-50. - -Lin D. An information-theoretic definition of similarity. in: Icml. 1998, 98(1998): 296-304. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} From 94d0fe92db91cdb28e97bb367841fb16970c57e1 Mon Sep 17 00:00:00 2001 From: Junpeng Zhang Date: Sun, 4 Feb 2024 23:01:29 +0800 Subject: [PATCH 2/3] Delete man directory --- man/BRCA_genes.Rd | 41 ---------- man/ceRExp.Rd | 31 -------- man/cor_binary.Rd | 46 ----------- man/mRExp.Rd | 31 -------- man/miRExp.Rd | 30 ------- man/miRSM.Rd | 151 ------------------------------------ man/miRSM_SS.Rd | 56 ------------- man/miRTarget.Rd | 32 -------- man/module_CEA.Rd | 44 ----------- man/module_Coexpress.Rd | 59 -------------- man/module_FA.Rd | 80 ------------------- man/module_GFA.Rd | 56 ------------- man/module_NMF.Rd | 54 ------------- man/module_ProNet.Rd | 71 ----------------- man/module_Validate.Rd | 35 --------- man/module_WGCNA.Rd | 48 ------------ man/module_biclust.Rd | 112 -------------------------- man/module_clust.Rd | 106 ------------------------- man/module_igraph.Rd | 57 -------------- man/module_miRdistribute.Rd | 33 -------- man/module_miRsponge.Rd | 31 -------- man/module_miRtarget.Rd | 36 --------- man/share_miRs.Rd | 34 -------- 23 files changed, 1274 deletions(-) delete mode 100644 man/BRCA_genes.Rd delete mode 100644 man/ceRExp.Rd delete mode 100644 man/cor_binary.Rd delete mode 100644 man/mRExp.Rd delete mode 100644 man/miRExp.Rd delete mode 100644 man/miRSM.Rd delete mode 100644 man/miRSM_SS.Rd delete mode 100644 man/miRTarget.Rd delete mode 100644 man/module_CEA.Rd delete mode 100644 man/module_Coexpress.Rd delete mode 100644 man/module_FA.Rd delete mode 100644 man/module_GFA.Rd delete mode 100644 man/module_NMF.Rd delete mode 100644 man/module_ProNet.Rd delete mode 100644 man/module_Validate.Rd delete mode 100644 man/module_WGCNA.Rd delete mode 100644 man/module_biclust.Rd delete mode 100644 man/module_clust.Rd delete mode 100644 man/module_igraph.Rd delete mode 100644 man/module_miRdistribute.Rd delete mode 100644 man/module_miRsponge.Rd delete mode 100644 man/module_miRtarget.Rd delete mode 100644 man/share_miRs.Rd diff --git a/man/BRCA_genes.Rd b/man/BRCA_genes.Rd deleted file mode 100644 index 655e742..0000000 --- a/man/BRCA_genes.Rd +++ /dev/null @@ -1,41 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{BRCA_genes} -\alias{BRCA_genes} -\title{BRCA genes} -\format{ -BRCA_genes: A SummarizedExperiment object with -4819 BRCA related genes (including lncRNAs and mRNAs). -} -\description{ -BRCA genes -} -\details{ -The BRCA related lncRNAs are from LncRNADisease v2.0, Lnc2Cancer v2.0 -and MNDR v2.0. The BRCA related mRNAs are from DisGeNET v5.0 and COSMIC v86. -} -\references{ -Bao Z, Yang Z, Huang Z, Zhou Y, Cui Q, Dong D. (2019) -"LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases". -Nucleic Acids Res., 47(D1):D1034-D1037. - -Cui T, Zhang L, Huang Y, Yi Y, Tan P, Zhao Y, Hu Y, Xu L, Li E, Wang D. -(2018) "MNDR v2.0: an updated resource of ncRNA-disease -associa-tions in mammals". Nucleic Acids Res., 46, D371-D374. - -Gao Y, Wang P, Wang Y, Ma X, Zhi H, Zhou D, Li X, Fang Y, Shen W, Xu Y, -Shang S, Wang L, Wang L, Ning S, Li X. (2019) "Lnc2Cancer v2.0: updated database of experimentally -supported long non-coding RNAs in human cancers". Nucleic Acids Res., 47, D1028-D1033. - -Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, Cole CG, -Ward S, Dawson E, Ponting L, Stefancsik R, Harsha B, Kok CY, Jia M, Jubb H, Sondka Z, -Thompson S, De T, Campbell PJ. (2017) "COSMIC: somatic cancer genetics at -high-resolution". Nucleic Acids Res., 45, D777-D783 - -Pinero J, Bravo A, Queralt-Rosinach N, Gutierrez-Sacristan A, Deu-Pons J, -Centeno E, Garcia-Garcia J, Sanz F, Furlong LI. -(2017) "DisGeNET: a comprehensive platform integrating -infor-mation on human disease-associated genes and variants". -Nucleic Acids Res., 45, D833-D839. -} diff --git a/man/ceRExp.Rd b/man/ceRExp.Rd deleted file mode 100644 index 2a42c37..0000000 --- a/man/ceRExp.Rd +++ /dev/null @@ -1,31 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{ceRExp} -\alias{ceRExp} -\title{ceRNA expression data} -\format{ -ceRExp: A SummarizedExperiment object with 72 BRCA -and 72 normal samples (rows) and 305 lncRNAs (columns). -} -\description{ -ceRNA expression data -} -\details{ -The matched breast invasive carcinoma (BRCA) miRNA, lncRNA -and mRNA expression data is obtained from TCGA -(http://cancergenome.nih.gov/). lncRNA expression data -is regarded as ceRNA expression data. The data focuses on -72 individuals for which the complete sets of -tumor and matched normal (i.e., normal tissue taken from the -same patient) profiles are available. -A lncRNA which has missing values in more than -10% of the samples is removed. The remaining missing values -are imputed using the k-nearest neighbours (KNN) algorithm -from the impute R package. We use the limma R package -to infer differentially expressed lncRNAs -between tumour and normal samples. After the analysis, -we select top 305 lncRNAs which are differentially expressed -at a significant level (adjusted p-value < 1E-02, -adjusted by Benjamini & Hochberg method). -} diff --git a/man/cor_binary.Rd b/man/cor_binary.Rd deleted file mode 100644 index 9210b57..0000000 --- a/man/cor_binary.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{cor_binary} -\alias{cor_binary} -\title{cor_binary} -\usage{ -cor_binary( - ceRExp, - mRExp = NULL, - cor.method = "pearson", - pos.p.value.cutoff = 0.01 -) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{cor.method}{The method of calculating correlation selected, -including 'pearson' (default), 'kendall', 'spearman'.} - -\item{pos.p.value.cutoff}{The significant p-value cutoff of -positive correlation.} -} -\value{ -A binary matrix. -} -\description{ -Generation of positively correlated binary matrix between -ceRNAs, or ceRNAs and mRNAs -} -\examples{ -data(BRCASampleData) -cor_binary_matrix <- cor_binary(ceRExp, mRExp) - -} -\references{ -Langfelder P, Horvath S. WGCNA: an R package for -weighted correlation network analysis. BMC Bioinformatics. -2008, 9:559. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/mRExp.Rd b/man/mRExp.Rd deleted file mode 100644 index e955903..0000000 --- a/man/mRExp.Rd +++ /dev/null @@ -1,31 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{mRExp} -\alias{mRExp} -\title{mRNA expression data} -\format{ -mRExp: A SummarizedExperiment -object with 72 BRCA and 72 normal samples (rows) and 226 miRNAs -(columns). -} -\description{ -mRNA expression data -} -\details{ -The matched breast invasive carcinoma (BRCA) miRNA, lncRNA -and mRNA expression data is obtained from TCGA -(http://cancergenome.nih.gov/). The data focuses on -72 individuals for which the complete sets of -tumor and matched normal (i.e., normal tissue taken from the -same patient) profiles are available. -A mRNA which has missing values in more than -10% of the samples is removed. The remaining missing values -are imputed using the k-nearest neighbours (KNN) algorithm -from the impute R package. We use the limma R package -to infer differentially expressed mRNAs -between tumour and normal samples. After the analysis, -we select top 500 mRNAs which are differentially expressed -at a significant level (adjusted p-value < 1E-02, -adjusted by Benjamini & Hochberg method). -} diff --git a/man/miRExp.Rd b/man/miRExp.Rd deleted file mode 100644 index 36cd3bd..0000000 --- a/man/miRExp.Rd +++ /dev/null @@ -1,30 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{miRExp} -\alias{miRExp} -\title{miRNA expression data} -\format{ -miRExp: A SummarizedExperiment object with 72 BRCA and 72 normal -samples (rows) and 226 miRNAs (columns). -} -\description{ -miRNA expression data -} -\details{ -The matched breast invasive carcinoma (BRCA) miRNA, lncRNA -and mRNA expression data is obtained from TCGA -(http://cancergenome.nih.gov/). The data focuses on -72 individuals for which the complete sets of -tumor and matched normal (i.e., normal tissue taken from the -same patient) profiles are available. -A miRNA which has missing values in more than -10% of the samples is removed. The remaining missing values -are imputed using the k-nearest neighbours (KNN) algorithm -from the impute R package. We use the limma R package -to infer differentially expressed miRNAs, ceRNAs and mRNAs -between tumour and normal samples. After the analysis, -we select top 226 miRNAs which are differentially expressed -at a significant level (adjusted p-value < 1E-02, -adjusted by Benjamini & Hochberg method). -} diff --git a/man/miRSM.Rd b/man/miRSM.Rd deleted file mode 100644 index bf96838..0000000 --- a/man/miRSM.Rd +++ /dev/null @@ -1,151 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{miRSM} -\alias{miRSM} -\title{miRSM} -\usage{ -miRSM( - miRExp, - ceRExp, - mRExp = NULL, - miRTarget, - CandidateModulegenes, - typex = "standard", - typez = "standard", - nperms = 100, - method = c("SCC", "SDC", "SRVC", "SM", "SSI", "SGCD", "SCRC"), - num_shared_miRNAs = 3, - pvalue.cutoff = 0.05, - MC.cutoff = 0.8, - SMC.cutoff = 0.1, - RV_method = c("RV", "RV2", "RVadjMaye", "RVadjGhaziri"), - BCmethod = "BCPlaid", - CRC_method = c("Coxhead", "Rozeboom") -) -} -\arguments{ -\item{miRExp}{A SummarizedExperiment object. miRNA expression data: -rows are samples and columns are miRNAs.} - -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{miRTarget}{A SummarizedExperiment object. Putative -miRNA-target binding information.} - -\item{CandidateModulegenes}{List object: a list of candidate -miRNA sponge modules. Only for the SCC, SDC, SRVC, SSI, SGCD and SCRC methods.} - -\item{typex}{The columns of x unordered (type='standard') or -ordered (type='ordered'). Only for the SCC method.} - -\item{typez}{The columns of z unordered (type='standard') or -ordered (type='ordered'). Only for the SCC method.} - -\item{nperms}{The number of permutations. Only for the SCC method.} - -\item{method}{The method selected to identify miRNA sponge -modules, including 'SCC', 'SDC', 'SRVC', 'SM', 'SSI', 'SGCD' and 'SCRC'.} - -\item{num_shared_miRNAs}{The number of common miRNAs shared -by a group of ceRNAs and mRNAs. Only for the SCC, SDC, SRVC, SSI, -SGCD and SCRC methods.} - -\item{pvalue.cutoff}{The p-value cutoff of significant sharing -of common miRNAs by a group of ceRNAs and mRNAs or significant correlation.} - -\item{MC.cutoff}{The cutoff of matrix correlation (canonical correlation, -distance correlation and RV coefficient). Only for the SCC, SDC, SRVC, -SSI, SGCD and SCRC methods.} - -\item{SMC.cutoff}{The cutoff of sensitivity matrix correlation -(sensitivity canonical correlation, sensitivity distance correlation -and sensitivity RV coefficient). Only for the SCC, SDC, SRVC, SSI, -SGCD and SCRC methods.} - -\item{RV_method}{the method of calculating RV coefficients. Select -one of 'RV', 'RV2', 'RVadjMaye' and 'RVadjGhaziri' methods. -Only for the SRVC method.} - -\item{BCmethod}{Specification of the biclustering method, -including 'BCBimax', 'BCCC', 'BCPlaid' (default), 'BCQuest', -'BCSpectral', 'BCXmotifs'. Only for the SM method.} - -\item{CRC_method}{the method of calculating matrix correlation. Select -one of 'Coxhead' and 'Rozeboom' methods. -Only for the SCRC method.} -} -\value{ -List object: Group competition of miRNA sponge modules, -and miRNA sponge modules. -} -\description{ -Identify miRNA sponge modules using sensitivity canonical correlation (SCC), -sensitivity distance correlation (SDC), -sensitivity RV coefficient (SRVC), sensitivity similarity index (SSI), -sensitivity generalized coefficient of determination (SGCD), -sensitivity Coxhead's or Rozeboom's coefficient (SCRC), -and sponge module (SM) methods. -} -\examples{ -data(BRCASampleData) -modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)], - mRExp[, seq_len(10)]) -# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) -miRSM_igraph_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, - modulegenes_igraph, method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV") - -} -\references{ -Witten DM, Tibshirani R, Hastie T. A penalized matrix -decomposition, with applications to sparse principal components -and canonical correlation analysis. Biostatistics. -2009, 10(3):515-34. - -Szekely GJ, Rizzo ML. Partial distance -correlation with methods for dissimilarities. Annals of Statistics. -2014, 42(6):2382-2412. - -Szekely GJ, Rizzo ML, Bakirov NK. -Measuring and Testing Dependence by Correlation of Distances, -Annals of Statistics, 2007, 35(6):2769-2794. - -Robert P, Escoufier Y. A unifying tool for -linear multivariate statistical methods: the RV-Coefficient. -Applied Statistics, 1976, 25(3):257-265. - -Smilde AK, Kiers HA, Bijlsma S, Rubingh CM, -van Erk MJ. Matrix correlations for high-dimensional -data: the modified RV-coefficient. Bioinformatics, -2009, 25(3):401-405. - -Maye CD, Lorent J, Horgan GW. -Exploratory analysis of multiple omics datasets using -the adjusted RV coefficient". Stat Appl Genet Mol Biol., -2011, 10, 14. - -EIGhaziri A, Qannari EM. Measures -of association between two datasets; Application to sensory data, -Food Quality and Preference, 2015, 40(A):116-124. - -Indahl UG, Næs T, Liland KH. A similarity index for -comparing coupled matrices. Journal of Chemometrics. 2018; 32:e3049. - -Yanai H. Unification of various techniques of multivariate -analysis by means of generalized coefficient of determination (GCD). -Journal of Behaviormetrics, 1974, 1(1): 45-54. - -Coxhead P. Measuring the relationship between two sets -of variables. British journal of mathematical and statistical psychology, -1974, 27(2): 205-212. - -Rozeboom WW. Linear correlations between sets of variables. -Psychometrika, 1965, 30(1): 57-71. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/miRSM_SS.Rd b/man/miRSM_SS.Rd deleted file mode 100644 index 8eba5a5..0000000 --- a/man/miRSM_SS.Rd +++ /dev/null @@ -1,56 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{miRSM_SS} -\alias{miRSM_SS} -\title{miRSM_SS} -\usage{ -miRSM_SS( - Modulelist.all, - Modulelist.exceptk, - sim.cutoff = 0.8, - sim.method = "Simpson" -) -} -\arguments{ -\item{Modulelist.all}{List object, modules using all of samples.} - -\item{Modulelist.exceptk}{List object, modules using all of samples excepting sample k.} - -\item{sim.cutoff}{Similarity cutoff between modules, the interval is [0 1].} - -\item{sim.method}{Methods for calculating similatiry between two modules, select one of three methods (Simpson, Jaccard and Lin). Default method is Simpson.} -} -\value{ -A list of sample-specific miRNA sponge modules -} -\description{ -Inferring sample-specific miRNA sponge modules -} -\examples{ -data(BRCASampleData) -nsamples <- 3 -modulegenes_igraph_all <- module_igraph(ceRExp[, 151:300], mRExp[, 151:300]) -modulegenes_WGCNA_exceptk <- lapply(seq(nsamples), function(i) - module_WGCNA(ceRExp[-i, seq(150)], - mRExp[-i, seq(150)])) - -miRSM_igraph_SRVC_all <- miRSM(miRExp, ceRExp[, 151:300], mRExp[, 151:300], - miRTarget, modulegenes_igraph_all, - method = "SRVC", SMC.cutoff = 0.01, - RV_method = "RV") -miRSM_WGCNA_SRVC_exceptk <- lapply(seq(nsamples), function(i) miRSM(miRExp[-i, ], - ceRExp[-i, seq(150)], mRExp[-i, seq(150)], - miRTarget, modulegenes_WGCNA_exceptk[[i]],#' - method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV")) - -Modulegenes_all <- miRSM_igraph_SRVC_all[[2]] -Modulegenes_exceptk <- lapply(seq(nsamples), function(i) - miRSM_WGCNA_SRVC_exceptk[[i]][[2]]) - -Modules_SS <- miRSM_SS(Modulegenes_all, Modulegenes_exceptk) - -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/miRTarget.Rd b/man/miRTarget.Rd deleted file mode 100644 index 19a87ee..0000000 --- a/man/miRTarget.Rd +++ /dev/null @@ -1,32 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{miRTarget} -\alias{miRTarget} -\title{miRNA-target ineractions} -\format{ -miRTarget: A SummarizedExperiment object with -29901 miRNA-target interactions. -} -\description{ -miRNA-target ineractions -} -\details{ -The miRNA-target binding information is -from miRTarBase v8.0 (http://mirtarbase.mbc.nctu.edu.tw/php/index.php), -and LncBase v2.0 -(http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2/index). -Among 226 miRNAs, 305 lncRNAs and 500 mRNAs -which are differentially expressed, we obtain 29901 miRNA-target -interactions (including miRNA-lncRNA and miRNA-mRNA interactions). -} -\references{ -Hastie T, Tibshirani R, Narasimhan B, Chu G. -impute: Imputation for microarray data. -R package version 1.54.0. doi: 10.18129/B9.bioc.impute. - -Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, -Shi W, et al. limma powers differential expression -analyses for RNA-sequencing and microarray studies. -Nucleic Acids Res. 2015; 43(7):e47. -} diff --git a/man/module_CEA.Rd b/man/module_CEA.Rd deleted file mode 100644 index 1b4adb3..0000000 --- a/man/module_CEA.Rd +++ /dev/null @@ -1,44 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_CEA} -\alias{module_CEA} -\title{module_CEA} -\usage{ -module_CEA(ceRExp, mRExp = NULL, Cancergenes, Modulelist) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{Cancergenes}{A SummarizedExperiment object: a list of cancer genes given.} - -\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} -} -\value{ -Cancer enrichment significance p-values of the identified miRNA sponge modules -} -\description{ -Cancer enrichment analysis of miRNA sponge modules using hypergeometric distribution test -} -\examples{ -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) -# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) -miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, - modulegenes_WGCNA, method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV") -miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] -miRSM.CEA.pvalue <- module_CEA(ceRExp, mRExp, BRCA_genes, - miRSM_WGCNA_SRVC_genes) - -} -\references{ -Johnson NL, Kotz S, Kemp AW (1992) -"Univariate Discrete Distributions", Second Edition. New York: Wiley. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_Coexpress.Rd b/man/module_Coexpress.Rd deleted file mode 100644 index 0c296fb..0000000 --- a/man/module_Coexpress.Rd +++ /dev/null @@ -1,59 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_Coexpress} -\alias{module_Coexpress} -\title{module_Coexpress} -\usage{ -module_Coexpress( - ceRExp, - mRExp = NULL, - Modulelist, - resample = 1000, - method = c("mean", "median"), - test.method = c("t.test", "wilcox.test") -) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} - -\item{resample}{The number of random miRNA sponge modules generated, and 1000 times in default.} - -\item{method}{The method used to evaluate the co-expression level of each miRNA sponge module. -Users can select "mean" or "median" to calculate co-expression value of each miRNA sponge module -and its corresponding random miRNA sponge module.} - -\item{test.method}{The method used to evaluate statistical significance p-value of -co-expression level higher than random miRNA sponge modules. -Users can select "t.test" or "wilcox.test" to calculate statistical significance p-value of -co-expression level higher than random miRNA sponge modules.} -} -\value{ -List object: co-expression values of miRNA sponge modules and their corresponding random miRNA sponge modules, -and statistical significance p-value of co-expression level higher than random miRNA sponge modules. -} -\description{ -Co-expression analysis of each miRNA sponge module and its corresponding random miRNA sponge modules -} -\examples{ -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) -# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) -miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, - modulegenes_WGCNA, method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV") -miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] -miRSM_WGCNA_Coexpress <- module_Coexpress(ceRExp, mRExp, - miRSM_WGCNA_SRVC_genes, - resample = 10, method = "mean", - test.method = "t.test") - -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_FA.Rd b/man/module_FA.Rd deleted file mode 100644 index d8f89f2..0000000 --- a/man/module_FA.Rd +++ /dev/null @@ -1,80 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_FA} -\alias{module_FA} -\title{module_FA} -\usage{ -module_FA( - Modulelist, - GOont = "BP", - Diseaseont = "DO", - KEGGorganism = "hsa", - Reactomeorganism = "human", - OrgDb = "org.Hs.eg.db", - padjustvaluecutoff = 0.05, - padjustedmethod = "BH", - Analysis.type = c("FEA", "DEA") -) -} -\arguments{ -\item{Modulelist}{List object: a list of miRNA sponge modules.} - -\item{GOont}{One of 'MF', 'BP', and 'CC' subontologies.} - -\item{Diseaseont}{One of 'DO', and 'DOLite' subontologies.} - -\item{KEGGorganism}{Organism, supported organism listed -in http://www.genome.jp/kegg/catalog/org_list.html.} - -\item{Reactomeorganism}{Organism, one of 'human', 'rat', ' -mouse', 'celegans', 'yeast', 'zebrafish', 'fly'.} - -\item{OrgDb}{OrgDb} - -\item{padjustvaluecutoff}{A cutoff value of adjusted p-values.} - -\item{padjustedmethod}{Adjusted method of p-values, can select -one of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', -'fdr', 'none'.} - -\item{Analysis.type}{The type of functional analysis selected, -including 'FEA' (functional enrichment analysis) and 'DEA' -(disease enrichment analysis).} -} -\value{ -List object: a list of enrichment analysis results. -} -\description{ -Functional analysis of miRNA sponge modules, including functional -enrichment and disease enrichment analysis -} -\examples{ -\dontrun{ -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) -# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) -miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, - modulegenes_WGCNA, method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV") -miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] -miRSM_WGCNA_SRVC_FEA <- module_FA(miRSM_WGCNA_SRVC_genes, Analysis.type = 'FEA') -miRSM_WGCNA_SRVC_DEA <- module_FA(miRSM_WGCNA_SRVC_genes, Analysis.type = 'DEA') -} - -} -\references{ -Zhang J, Liu L, Xu T, Xie Y, Zhao C, Li J, Le TD (2019). -“miRspongeR: an R/Bioconductor package for the identification and analysis of -miRNA sponge interaction networks and modules.” BMC Bioinformatics, 20, 235. - -Zhang J, Liu L, Zhang W, Li X, Zhao C, Li S, Li J, Le TD. -miRspongeR 2.0: an enhanced R package for exploring miRNA sponge regulation. -Bioinform Adv. 2022 Sep 2;2(1):vbac063. - -Yu G, Wang L, Han Y, He Q (2012). -“clusterProfiler: an R package for comparing biological themes among gene clusters.” -OMICS: A Journal of Integrative Biology, 16(5), 284-287. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_GFA.Rd b/man/module_GFA.Rd deleted file mode 100644 index c029ae6..0000000 --- a/man/module_GFA.Rd +++ /dev/null @@ -1,56 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_GFA} -\alias{module_GFA} -\title{module_GFA} -\usage{ -module_GFA( - ceRExp, - mRExp = NULL, - StrengthCut = 0.9, - iter.max = 5000, - num.ModuleceRs = 2, - num.ModulemRs = 2 -) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{StrengthCut}{Desired minimum strength (absolute value of -association with interval [0 1]) for each bicluster.} - -\item{iter.max}{The total number of Gibbs sampling steps -(default 1000).} - -\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} - -\item{num.ModulemRs}{The minimum number of mRNAs in each module.} -} -\value{ -GeneSetCollection object: a list of module genes. -} -\description{ -Identification of gene modules from matched ceRNA and mRNA -expression data using GFA package -} -\examples{ -data(BRCASampleData) -modulegenes_GFA <- module_GFA(ceRExp[seq_len(20), seq_len(15)], - mRExp[seq_len(20), seq_len(15)], iter.max = 2600) - -} -\references{ -Bunte K, Lepp\'{a}aho E, Saarinen I, Kaski S. -Sparse group factor analysis for biclustering of multiple data sources. Bioinformatics. 2016, 32(16):2457-63. - -Lepp\'{a}aho E, Ammad-ud-din M, Kaski S. GFA: -exploratory analysis of multiple data sources with group factor -analysis. J Mach Learn Res. 2017, 18(39):1-5. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_NMF.Rd b/man/module_NMF.Rd deleted file mode 100644 index cf9b0fa..0000000 --- a/man/module_NMF.Rd +++ /dev/null @@ -1,54 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_NMF} -\alias{module_NMF} -\title{module_NMF} -\usage{ -module_NMF( - ceRExp, - mRExp = NULL, - NMF.algorithm = "brunet", - num.modules = 10, - num.ModuleceRs = 2, - num.ModulemRs = 2 -) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{NMF.algorithm}{Specification of the NMF algorithm, -including 'brunet' (default), 'Frobenius', 'KL', 'lee', 'nsNMF', -'offset', 'siNMF', 'snmf/l', 'snmf/r'.} - -\item{num.modules}{The number of modules to be identified.} - -\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} - -\item{num.ModulemRs}{The minimum number of mRNAs in each module.} -} -\value{ -GeneSetCollection object: a list of module genes. -} -\description{ -Identification of gene modules from matched ceRNA and mRNA -expression data using NMF package -} -\examples{ -data(BRCASampleData) -# Reimport NMF package to avoid conflicts with DelayedArray package -library(NMF) -modulegenes_NMF <- module_NMF(ceRExp[, seq_len(10)], - mRExp[, seq_len(10)]) - -} -\references{ -Gaujoux R, Seoighe C. A flexible R package for -nonnegative matrix factorization. BMC Bioinformatics. 2010, 11:367. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_ProNet.Rd b/man/module_ProNet.Rd deleted file mode 100644 index 877c4e7..0000000 --- a/man/module_ProNet.Rd +++ /dev/null @@ -1,71 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_ProNet} -\alias{module_ProNet} -\title{module_ProNet} -\usage{ -module_ProNet( - ceRExp, - mRExp = NULL, - cor.method = "pearson", - pos.p.value.cutoff = 0.01, - cluster.method = "MCL", - num.ModuleceRs = 2, - num.ModulemRs = 2 -) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{cor.method}{The method of calculating correlation selected, -including 'pearson' (default), 'kendall', 'spearman'.} - -\item{pos.p.value.cutoff}{The significant p-value cutoff of -positive correlation} - -\item{cluster.method}{The clustering method selected in -\pkg{ProNet} package, including 'FN', 'MCL' (default), -'LINKCOMM', 'MCODE'.} - -\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} - -\item{num.ModulemRs}{The minimum number of mRNAs in each module.} -} -\value{ -GeneSetCollection object: a list of module genes. -} -\description{ -Identification of gene modules from matched ceRNA and mRNA -expression data using ProNet package -} -\examples{ -data(BRCASampleData) -modulegenes_ProNet <- module_ProNet(ceRExp[, seq_len(10)], - mRExp[, seq_len(10)]) - -} -\references{ -Clauset A, Newman ME, Moore C. Finding community -structure in very large networks. Phys Rev E Stat Nonlin Soft -Matter Phys., 2004, 70(6 Pt 2):066111. - -Enright AJ, Van Dongen S, Ouzounis CA. An efficient -algorithm for large-scale detection of protein families. -Nucleic Acids Res., 2002, 30(7):1575-84. - -Kalinka AT, Tomancak P. linkcomm: an R package -for the generation, visualization, and analysis of link -communities in networks of arbitrary size and type. -Bioinformatics, 2011, 27(14):2011-2. - -Bader GD, Hogue CW. An automated method for -finding molecular complexes in large protein interaction -networks. BMC Bioinformatics, 2003, 4:2. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_Validate.Rd b/man/module_Validate.Rd deleted file mode 100644 index 92a860b..0000000 --- a/man/module_Validate.Rd +++ /dev/null @@ -1,35 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_Validate} -\alias{module_Validate} -\title{module_Validate} -\usage{ -module_Validate(Modulelist, Groundtruth) -} -\arguments{ -\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} - -\item{Groundtruth}{Matrix object: a list of experimentally validated miRNA sponge interactions.} -} -\value{ -List object: a list of validated miRNA sponge interactions in each miRNA sponge module -} -\description{ -Validation of miRNA sponge interactions in each miRNA sponge module -} -\examples{ -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) -# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) -miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, - modulegenes_WGCNA, method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV") -miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] -Groundtruthcsv <- system.file("extdata", "Groundtruth.csv", package="miRSM") -Groundtruth <- read.csv(Groundtruthcsv, header=TRUE, sep=",") -miRSM.Validate <- module_Validate(miRSM_WGCNA_SRVC_genes, Groundtruth) - -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_WGCNA.Rd b/man/module_WGCNA.Rd deleted file mode 100644 index 17f01f7..0000000 --- a/man/module_WGCNA.Rd +++ /dev/null @@ -1,48 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_WGCNA} -\alias{module_WGCNA} -\title{module_WGCNA} -\usage{ -module_WGCNA( - ceRExp, - mRExp = NULL, - RsquaredCut = 0.9, - num.ModuleceRs = 2, - num.ModulemRs = 2 -) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{RsquaredCut}{Desired minimum scale free topology fitting index -R^2 with interval [0 1].} - -\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} - -\item{num.ModulemRs}{The minimum number of mRNAs in each module.} -} -\value{ -GeneSetCollection object: a list of module genes. -} -\description{ -Identification of co-expressed gene modules from matched ceRNA and mRNA -expression data using WGCNA package -} -\examples{ -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp[, seq_len(80)], - mRExp[, seq_len(80)]) - -} -\references{ -Langfelder P, Horvath S. WGCNA: an R package for weighted -correlation network analysis. BMC Bioinformatics. 2008, 9:559.#' -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_biclust.Rd b/man/module_biclust.Rd deleted file mode 100644 index 50223b4..0000000 --- a/man/module_biclust.Rd +++ /dev/null @@ -1,112 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_biclust} -\alias{module_biclust} -\title{module_biclust} -\usage{ -module_biclust( - ceRExp, - mRExp = NULL, - BCmethod = "fabia", - num.modules = 10, - num.ModuleceRs = 2, - num.ModulemRs = 2 -) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{BCmethod}{Specification of the biclustering method, -including 'BCBimax', 'BCCC', 'BCPlaid' (default), 'BCQuest', -'BCSpectral', 'BCXmotifs', iBBiG', 'fabia', 'fabiap', -'fabias', 'mfsc', 'nmfdiv', 'nmfeu', 'nmfsc', 'FLOC', 'isa', -'BCs4vd', 'BCssvd', 'bibit' and 'quBicluster'.} - -\item{num.modules}{The number of modules to be identified. For the 'BCPlaid', -'BCSpectral', 'isa' and 'bibit' methods, no need to set the parameter. For the -'quBicluster' method, the parameter is used to set the number of biclusters -that should be reported.} - -\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} - -\item{num.ModulemRs}{The minimum number of mRNAs in each module.} -} -\value{ -GeneSetCollection object: a list of module genes. -} -\description{ -Identification of gene modules from matched ceRNA and mRNA -expression data using a series of biclustering packages, -including biclust, iBBiG, fabia, BicARE, isa2, s4vd, -BiBitR and rqubic -} -\examples{ -data(BRCASampleData) -modulegenes_biclust <- module_biclust(ceRExp[, seq_len(30)], - mRExp[, seq_len(30)]) - -} -\references{ -Preli\'{c} A, Bleuler S, Zimmermann P, Wille A, -B\'{u}hlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E. -A systematic comparison and evaluation of biclustering methods -for gene expression data. Bioinformatics. 2006, 22(9):1122-9. - -Cheng Y, Church GM. Biclustering of expression data. -Proc Int Conf Intell Syst Mol Biol. 2000, 8:93-103. - -Turner H, Bailey T, Krzanowski W. Improved -biclustering of microarray data demonstrated through systematic -performance tests. Comput Stat Data Anal. 2003, 48(2): 235-254. - -Murali TM, Kasif S. Extracting conserved gene -expression motifs from gene expression data. -Pac Symp Biocomput. 2003:77-88. - -Kluger Y, Basri R, Chang JT, Gerstein M. -Spectral biclustering of microarray data: coclustering genes -and conditions. Genome Res. 2003, 13(4):703-16. - -Gusenleitner D, Howe EA, Bentink S, Quackenbush J, -Culhane AC. iBBiG: iterative binary bi-clustering of gene sets. -Bioinformatics. 2012, 28(19):2484-92. - -Hochreiter S, Bodenhofer U, Heusel M, Mayr A, -Mitterecker A, Kasim A, Khamiakova T, Van Sanden S, Lin D, -Talloen W, Bijnens L, G\'{o}hlmann HW, Shkedy Z, Clevert DA. -FABIA: factor analysis for bicluster acquisition. -Bioinformatics. 2010, 26(12):1520-7. - -Yang J, Wang H, Wang W, Yu, PS. An improved -biclustering method for analyzing gene expression. -Int J Artif Intell Tools. 2005, 14(5): 771-789. - -Bergmann S, Ihmels J, Barkai N. Iterative -signature algorithm for the analysis of large-scale gene -expression data. Phys Rev E Stat Nonlin Soft Matter Phys. -2003, 67(3 Pt 1):031902. - -Sill M, Kaiser S, Benner A, Kopp-Schneider A. -Robust biclustering by sparse singular value decomposition -incorporating stability selection. Bioinformatics. 2011, -27(15):2089-97. - -Lee M, Shen H, Huang JZ, Marron JS. Biclustering -via sparse singular value decomposition. Biometrics. 2010, -66(4):1087-95. - -Rodriguez-Baena DS, Perez-Pulido AJ, Aguilar-Ruiz JS. -A biclustering algorithm for extracting bit-patterns from -binary datasets. Bioinformatics. 2011, 27(19):2738-45. - -Li G, Ma Q, Tang H, Paterson AH, Xu Y. -QUBIC: a qualitative biclustering algorithm for analyses of -gene expression data. Nucleic Acids Res. 2009, 37(15):e101. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_clust.Rd b/man/module_clust.Rd deleted file mode 100644 index bbe2a2d..0000000 --- a/man/module_clust.Rd +++ /dev/null @@ -1,106 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_clust} -\alias{module_clust} -\title{module_clust} -\usage{ -module_clust( - ceRExp, - mRExp = NULL, - cluster.method = "kmeans", - num.modules = 10, - num.ModuleceRs = 2, - num.ModulemRs = 2 -) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{cluster.method}{Specification of the clustering method, -including 'kmeans'(default), 'hclust', 'dbscan' , 'clique', -'gmm', 'som' and 'fcm'.} - -\item{num.modules}{Parameter of the number of modules to be identified -for the 'kmeans', 'hclust', 'gmm' and 'fcm' methods. Parameter of the number -of intervals for the 'clique' method. For the 'dbscan' and 'som' methods, -no need to set the parameter.} - -\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} - -\item{num.ModulemRs}{The minimum number of mRNAs in each module.} -} -\value{ -GeneSetCollection object: a list of module genes. -} -\description{ -Identification of gene modules from matched ceRNA and mRNA -expression data using a series of clustering packages, -including stats, flashClust, dbscan, subspace, mclust, SOMbrero and ppclust packages. -} -\examples{ -data(BRCASampleData) -modulegenes_clust <- module_clust(ceRExp[, seq_len(30)], - mRExp[, seq_len(30)]) - -} -\references{ -Forgy EW. Cluster analysis of multivariate -data: efficiency vs interpretability of classifications. -Biometrics, 1965, 21:768-769. - -Hartigan JA, Wong MA. -Algorithm AS 136: A K-means clustering algorithm. -Applied Statistics, 1979, 28:100-108. - -Lloyd SP. Least squares quantization in PCM. -Technical Note, Bell Laboratories. Published in 1982 -in IEEE Transactions on Information Theory, 1982, 28:128-137. - -MacQueen J. Some methods for classification -and analysis of multivariate observations. -In Proceedings of the Fifth Berkeley Symposium on -Mathematical Statistics and Probability, -eds L. M. Le Cam & J. Neyman, 1967, 1, pp.281-297. -Berkeley, CA: University of California Press. - -Langfelder P, Horvath S. Fast R Functions for -Robust Correlations and Hierarchical Clustering. -Journal of Statistical Software. 2012, 46(11):1-17. - -Ester M, Kriegel HP, Sander J, Xu X. A density-based -algorithm for discovering clusters in large spatial databases with -noise, Proceedings of 2nd International Conference on Knowledge Discovery and -Data Mining (KDD-96), 1996, 96(34): 226-231. - -Campello RJGB, Moulavi D, Sander J. -Density-based clustering based on hierarchical density estimates, -Pacific-Asia conference on knowledge discovery and data mining. -Springer, Berlin, Heidelberg, 2013: 160-172. - -Agrawal R, Gehrke J, Gunopulos D, Raghavan P. -Automatic subspace clustering of high dimensional data for -data mining applications. In Proc. ACM SIGMOD, 1998. - -Scrucca L, Fop M, Murphy TB, Raftery AE. -mclust 5: clustering, classification and density estimation using -Gaussian finite mixture models The R Journal 8/1, 2016, pp. 205-233. - -Kohonen T. Self-Organizing Maps. -Berlin/Heidelberg: Springer-Verlag, 3rd edition, 2001. - -Dunn JC. A fuzzy relative of the ISODATA process -and its use in detecting compact well-separated clusters. Journal of Cybernetics, -1973, 3(3):32-57. - -Bezdek JC. Cluster validity with fuzzy sets. Journal of Cybernetics, 1974, 3: 58-73. - -Bezdek JC. Pattern recognition with fuzzy objective function -algorithms. Plenum, NY, 1981. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_igraph.Rd b/man/module_igraph.Rd deleted file mode 100644 index 543c8ee..0000000 --- a/man/module_igraph.Rd +++ /dev/null @@ -1,57 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_igraph} -\alias{module_igraph} -\title{module_igraph} -\usage{ -module_igraph( - ceRExp, - mRExp = NULL, - cor.method = "pearson", - pos.p.value.cutoff = 0.01, - cluster.method = "greedy", - num.ModuleceRs = 2, - num.ModulemRs = 2 -) -} -\arguments{ -\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: -rows are samples and columns are ceRNAs.} - -\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: -rows are samples and columns are mRNAs.} - -\item{cor.method}{The method of calculating correlation selected, -including 'pearson' (default), 'kendall', 'spearman'.} - -\item{pos.p.value.cutoff}{The significant p-value cutoff of -positive correlation.} - -\item{cluster.method}{The clustering method selected in -\pkg{igraph} package, including 'betweenness', 'greedy' (default), -'infomap', 'prop', 'eigen', 'louvain', 'walktrap'.} - -\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} - -\item{num.ModulemRs}{The minimum number of mRNAs in each module.} -} -\value{ -GeneSetCollection object: a list of module genes. -} -\description{ -Identification of gene modules from matched ceRNA and mRNA -expression data using igraph package -} -\examples{ -data(BRCASampleData) -modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)], - mRExp[, seq_len(10)]) - -} -\references{ -Csardi G, Nepusz T. The igraph software package for -complex network research, InterJournal, Complex Systems. 2006:1695. -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_miRdistribute.Rd b/man/module_miRdistribute.Rd deleted file mode 100644 index 0fa1d89..0000000 --- a/man/module_miRdistribute.Rd +++ /dev/null @@ -1,33 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_miRdistribute} -\alias{module_miRdistribute} -\title{module_miRdistribute} -\usage{ -module_miRdistribute(share_miRs) -} -\arguments{ -\item{share_miRs}{List object: a list of common miRNAs of each miRNA sponge module -generated by share_miRs function.} -} -\value{ -Matrix object: miRNA distribution in each miRNA sponge module. -} -\description{ -miRNA distribution analysis of sharing miRNAs by the identified miRNA sponge modules -} -\examples{ -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) -# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) -miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, - modulegenes_WGCNA, method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV") -miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] -miRSM_WGCNA_share_miRs <- share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes) -miRSM_WGCNA_miRdistribute <- module_miRdistribute(miRSM_WGCNA_share_miRs) - -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_miRsponge.Rd b/man/module_miRsponge.Rd deleted file mode 100644 index 93b3162..0000000 --- a/man/module_miRsponge.Rd +++ /dev/null @@ -1,31 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_miRsponge} -\alias{module_miRsponge} -\title{module_miRsponge} -\usage{ -module_miRsponge(Modulelist) -} -\arguments{ -\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} -} -\value{ -List object: miRNA sponge interactions of each miRNA sponge module. -} -\description{ -Extract miRNA sponge interactions of each miRNA sponge module -} -\examples{ -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) -# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) -miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, - modulegenes_WGCNA, method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV") -miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] -miRSM_WGCNA_miRsponge <- module_miRsponge(miRSM_WGCNA_SRVC_genes) - -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/module_miRtarget.Rd b/man/module_miRtarget.Rd deleted file mode 100644 index b78cbee..0000000 --- a/man/module_miRtarget.Rd +++ /dev/null @@ -1,36 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{module_miRtarget} -\alias{module_miRtarget} -\title{module_miRtarget} -\usage{ -module_miRtarget(share_miRs, Modulelist) -} -\arguments{ -\item{share_miRs}{List object: a list of common miRNAs of each miRNA sponge module -generated by share_miRs function.} - -\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} -} -\value{ -List object: miRNA-target interactions of each miRNA sponge module. -} -\description{ -Extract miRNA-target interactions of each miRNA sponge module -} -\examples{ -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) -# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) -miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, - modulegenes_WGCNA, method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV") -miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] -miRSM_WGCNA_share_miRs <- share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes) -miRSM_WGCNA_miRtarget <- module_miRtarget(miRSM_WGCNA_share_miRs, - miRSM_WGCNA_SRVC_genes) - -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} diff --git a/man/share_miRs.Rd b/man/share_miRs.Rd deleted file mode 100644 index 11d6de5..0000000 --- a/man/share_miRs.Rd +++ /dev/null @@ -1,34 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/miRSM.R -\name{share_miRs} -\alias{share_miRs} -\title{share_miRs} -\usage{ -share_miRs(miRTarget, Modulelist) -} -\arguments{ -\item{miRTarget}{A SummarizedExperiment object. Putative -miRNA-target binding information.} - -\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} -} -\value{ -List object: a list of common miRNAs of each miRNA sponge module. -} -\description{ -Extract common miRNAs of each miRNA sponge module -} -\examples{ -data(BRCASampleData) -modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) -# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) -miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, - modulegenes_WGCNA, method = "SRVC", - SMC.cutoff = 0.01, RV_method = "RV") -miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] -miRSM_WGCNA_share_miRs <- share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes) - -} -\author{ -Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) -} From da56f8765cee1d9cc8d7b316fe66ad5876cf7c60 Mon Sep 17 00:00:00 2001 From: Junpeng Zhang Date: Sun, 4 Feb 2024 23:02:12 +0800 Subject: [PATCH 3/3] Add files via upload Update --- man/BRCA_genes.Rd | 41 ++++++++++ man/ceRExp.Rd | 31 ++++++++ man/cor_binary.Rd | 46 +++++++++++ man/diff_module.Rd | 39 ++++++++++ man/mRExp.Rd | 31 ++++++++ man/miRExp.Rd | 30 +++++++ man/miRSM.Rd | 151 ++++++++++++++++++++++++++++++++++++ man/miRSM_SS.Rd | 56 +++++++++++++ man/miRTarget.Rd | 32 ++++++++ man/module_CEA.Rd | 44 +++++++++++ man/module_Coexpress.Rd | 59 ++++++++++++++ man/module_FA.Rd | 80 +++++++++++++++++++ man/module_GFA.Rd | 56 +++++++++++++ man/module_NMF.Rd | 54 +++++++++++++ man/module_ProNet.Rd | 71 +++++++++++++++++ man/module_Validate.Rd | 35 +++++++++ man/module_WGCNA.Rd | 48 ++++++++++++ man/module_biclust.Rd | 112 ++++++++++++++++++++++++++ man/module_clust.Rd | 106 +++++++++++++++++++++++++ man/module_group_sim.Rd | 39 ++++++++++ man/module_igraph.Rd | 57 ++++++++++++++ man/module_miRdistribute.Rd | 33 ++++++++ man/module_miRsponge.Rd | 31 ++++++++ man/module_miRtarget.Rd | 36 +++++++++ man/share_miRs.Rd | 34 ++++++++ 25 files changed, 1352 insertions(+) create mode 100644 man/BRCA_genes.Rd create mode 100644 man/ceRExp.Rd create mode 100644 man/cor_binary.Rd create mode 100644 man/diff_module.Rd create mode 100644 man/mRExp.Rd create mode 100644 man/miRExp.Rd create mode 100644 man/miRSM.Rd create mode 100644 man/miRSM_SS.Rd create mode 100644 man/miRTarget.Rd create mode 100644 man/module_CEA.Rd create mode 100644 man/module_Coexpress.Rd create mode 100644 man/module_FA.Rd create mode 100644 man/module_GFA.Rd create mode 100644 man/module_NMF.Rd create mode 100644 man/module_ProNet.Rd create mode 100644 man/module_Validate.Rd create mode 100644 man/module_WGCNA.Rd create mode 100644 man/module_biclust.Rd create mode 100644 man/module_clust.Rd create mode 100644 man/module_group_sim.Rd create mode 100644 man/module_igraph.Rd create mode 100644 man/module_miRdistribute.Rd create mode 100644 man/module_miRsponge.Rd create mode 100644 man/module_miRtarget.Rd create mode 100644 man/share_miRs.Rd diff --git a/man/BRCA_genes.Rd b/man/BRCA_genes.Rd new file mode 100644 index 0000000..3d00c02 --- /dev/null +++ b/man/BRCA_genes.Rd @@ -0,0 +1,41 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{BRCA_genes} +\alias{BRCA_genes} +\title{BRCA genes} +\format{ +BRCA_genes: A SummarizedExperiment object with +4819 BRCA related genes (including lncRNAs and mRNAs). +} +\description{ +BRCA genes +} +\details{ +The BRCA related lncRNAs are from LncRNADisease v2.0, Lnc2Cancer v2.0 +and MNDR v2.0. The BRCA related mRNAs are from DisGeNET v5.0 and COSMIC v86. +} +\references{ +Bao Z, Yang Z, Huang Z, Zhou Y, Cui Q, Dong D. (2019) +"LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases". +Nucleic Acids Res., 47(D1):D1034-D1037. + +Cui T, Zhang L, Huang Y, Yi Y, Tan P, Zhao Y, Hu Y, Xu L, Li E, Wang D. +(2018) "MNDR v2.0: an updated resource of ncRNA-disease +associa-tions in mammals". Nucleic Acids Res., 46, D371-D374. + +Gao Y, Wang P, Wang Y, Ma X, Zhi H, Zhou D, Li X, Fang Y, Shen W, Xu Y, +Shang S, Wang L, Wang L, Ning S, Li X. (2019) "Lnc2Cancer v2.0: updated database of experimentally +supported long non-coding RNAs in human cancers". Nucleic Acids Res., 47, D1028-D1033. + +Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, Cole CG, +Ward S, Dawson E, Ponting L, Stefancsik R, Harsha B, Kok CY, Jia M, Jubb H, Sondka Z, +Thompson S, De T, Campbell PJ. (2017) "COSMIC: somatic cancer genetics at +high-resolution". Nucleic Acids Res., 45, D777-D783 + +Pinero J, Bravo A, Queralt-Rosinach N, Gutierrez-Sacristan A, Deu-Pons J, +Centeno E, Garcia-Garcia J, Sanz F, Furlong LI. +(2017) "DisGeNET: a comprehensive platform integrating +infor-mation on human disease-associated genes and variants". +Nucleic Acids Res., 45, D833-D839. +} diff --git a/man/ceRExp.Rd b/man/ceRExp.Rd new file mode 100644 index 0000000..f987d54 --- /dev/null +++ b/man/ceRExp.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{ceRExp} +\alias{ceRExp} +\title{ceRNA expression data} +\format{ +ceRExp: A SummarizedExperiment object with 72 BRCA +and 72 normal samples (rows) and 305 lncRNAs (columns). +} +\description{ +ceRNA expression data +} +\details{ +The matched breast invasive carcinoma (BRCA) miRNA, lncRNA +and mRNA expression data is obtained from TCGA +(http://cancergenome.nih.gov/). lncRNA expression data +is regarded as ceRNA expression data. The data focuses on +72 individuals for which the complete sets of +tumor and matched normal (i.e., normal tissue taken from the +same patient) profiles are available. +A lncRNA which has missing values in more than +10% of the samples is removed. The remaining missing values +are imputed using the k-nearest neighbours (KNN) algorithm +from the impute R package. We use the limma R package +to infer differentially expressed lncRNAs +between tumour and normal samples. After the analysis, +we select top 305 lncRNAs which are differentially expressed +at a significant level (adjusted p-value < 1E-02, +adjusted by Benjamini & Hochberg method). +} diff --git a/man/cor_binary.Rd b/man/cor_binary.Rd new file mode 100644 index 0000000..235707b --- /dev/null +++ b/man/cor_binary.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{cor_binary} +\alias{cor_binary} +\title{cor_binary} +\usage{ +cor_binary( + ceRExp, + mRExp = NULL, + cor.method = "pearson", + pos.p.value.cutoff = 0.01 +) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{cor.method}{The method of calculating correlation selected, +including 'pearson' (default), 'kendall', 'spearman'.} + +\item{pos.p.value.cutoff}{The significant p-value cutoff of +positive correlation.} +} +\value{ +A binary matrix. +} +\description{ +Generation of positively correlated binary matrix between +ceRNAs, or ceRNAs and mRNAs +} +\examples{ +data(BRCASampleData) +cor_binary_matrix <- cor_binary(ceRExp, mRExp) + +} +\references{ +Langfelder P, Horvath S. WGCNA: an R package for +weighted correlation network analysis. BMC Bioinformatics. +2008, 9:559. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/diff_module.Rd b/man/diff_module.Rd new file mode 100644 index 0000000..010238c --- /dev/null +++ b/man/diff_module.Rd @@ -0,0 +1,39 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{diff_module} +\alias{diff_module} +\title{diff_module} +\usage{ +diff_module( + Module.group1, + Module.group2, + sim.cutoff = 0.8, + sim.method = "Simpson" +) +} +\arguments{ +\item{Module.group1}{List object, the first list of module group.} + +\item{Module.group2}{List object, the second list of module group.} + +\item{sim.cutoff}{Similarity cutoff between modules, the interval is [0 1].} + +\item{sim.method}{Methods for calculating similatiry between two modules, select one of three methods (Simpson, Jaccard and Lin). Default method is Simpson.} +} +\value{ +A list of differential modules +} +\description{ +Inferring differential modules between two list of module groups +} +\examples{ +library(GSEABase) +data(BRCASampleData) +modulegenes_WGCNA_all <- module_WGCNA(ceRExp, mRExp) +modulegenes_WGCNA_1 <- module_WGCNA(ceRExp[-1, ], mRExp[-1, ]) +Differential_module <- diff_module(geneIds(modulegenes_WGCNA_all), geneIds(modulegenes_WGCNA_1)) + +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/mRExp.Rd b/man/mRExp.Rd new file mode 100644 index 0000000..f4d190f --- /dev/null +++ b/man/mRExp.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{mRExp} +\alias{mRExp} +\title{mRNA expression data} +\format{ +mRExp: A SummarizedExperiment +object with 72 BRCA and 72 normal samples (rows) and 226 miRNAs +(columns). +} +\description{ +mRNA expression data +} +\details{ +The matched breast invasive carcinoma (BRCA) miRNA, lncRNA +and mRNA expression data is obtained from TCGA +(http://cancergenome.nih.gov/). The data focuses on +72 individuals for which the complete sets of +tumor and matched normal (i.e., normal tissue taken from the +same patient) profiles are available. +A mRNA which has missing values in more than +10% of the samples is removed. The remaining missing values +are imputed using the k-nearest neighbours (KNN) algorithm +from the impute R package. We use the limma R package +to infer differentially expressed mRNAs +between tumour and normal samples. After the analysis, +we select top 500 mRNAs which are differentially expressed +at a significant level (adjusted p-value < 1E-02, +adjusted by Benjamini & Hochberg method). +} diff --git a/man/miRExp.Rd b/man/miRExp.Rd new file mode 100644 index 0000000..5103527 --- /dev/null +++ b/man/miRExp.Rd @@ -0,0 +1,30 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{miRExp} +\alias{miRExp} +\title{miRNA expression data} +\format{ +miRExp: A SummarizedExperiment object with 72 BRCA and 72 normal +samples (rows) and 226 miRNAs (columns). +} +\description{ +miRNA expression data +} +\details{ +The matched breast invasive carcinoma (BRCA) miRNA, lncRNA +and mRNA expression data is obtained from TCGA +(http://cancergenome.nih.gov/). The data focuses on +72 individuals for which the complete sets of +tumor and matched normal (i.e., normal tissue taken from the +same patient) profiles are available. +A miRNA which has missing values in more than +10% of the samples is removed. The remaining missing values +are imputed using the k-nearest neighbours (KNN) algorithm +from the impute R package. We use the limma R package +to infer differentially expressed miRNAs, ceRNAs and mRNAs +between tumour and normal samples. After the analysis, +we select top 226 miRNAs which are differentially expressed +at a significant level (adjusted p-value < 1E-02, +adjusted by Benjamini & Hochberg method). +} diff --git a/man/miRSM.Rd b/man/miRSM.Rd new file mode 100644 index 0000000..51bc93d --- /dev/null +++ b/man/miRSM.Rd @@ -0,0 +1,151 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{miRSM} +\alias{miRSM} +\title{miRSM} +\usage{ +miRSM( + miRExp, + ceRExp, + mRExp = NULL, + miRTarget, + CandidateModulegenes, + typex = "standard", + typez = "standard", + nperms = 100, + method = c("SCC", "SDC", "SRVC", "SM", "SSI", "SGCD", "SCRC"), + num_shared_miRNAs = 3, + pvalue.cutoff = 0.05, + MC.cutoff = 0.8, + SMC.cutoff = 0.1, + RV_method = c("RV", "RV2", "RVadjMaye", "RVadjGhaziri"), + BCmethod = "BCPlaid", + CRC_method = c("Coxhead", "Rozeboom") +) +} +\arguments{ +\item{miRExp}{A SummarizedExperiment object. miRNA expression data: +rows are samples and columns are miRNAs.} + +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{miRTarget}{A SummarizedExperiment object. Putative +miRNA-target binding information.} + +\item{CandidateModulegenes}{List object: a list of candidate +miRNA sponge modules. Only for the SCC, SDC, SRVC, SSI, SGCD and SCRC methods.} + +\item{typex}{The columns of x unordered (type='standard') or +ordered (type='ordered'). Only for the SCC method.} + +\item{typez}{The columns of z unordered (type='standard') or +ordered (type='ordered'). Only for the SCC method.} + +\item{nperms}{The number of permutations. Only for the SCC method.} + +\item{method}{The method selected to identify miRNA sponge +modules, including 'SCC', 'SDC', 'SRVC', 'SM', 'SSI', 'SGCD' and 'SCRC'.} + +\item{num_shared_miRNAs}{The number of common miRNAs shared +by a group of ceRNAs and mRNAs. Only for the SCC, SDC, SRVC, SSI, +SGCD and SCRC methods.} + +\item{pvalue.cutoff}{The p-value cutoff of significant sharing +of common miRNAs by a group of ceRNAs and mRNAs or significant correlation.} + +\item{MC.cutoff}{The cutoff of matrix correlation (canonical correlation, +distance correlation and RV coefficient). Only for the SCC, SDC, SRVC, +SSI, SGCD and SCRC methods.} + +\item{SMC.cutoff}{The cutoff of sensitivity matrix correlation +(sensitivity canonical correlation, sensitivity distance correlation +and sensitivity RV coefficient). Only for the SCC, SDC, SRVC, SSI, +SGCD and SCRC methods.} + +\item{RV_method}{the method of calculating RV coefficients. Select +one of 'RV', 'RV2', 'RVadjMaye' and 'RVadjGhaziri' methods. +Only for the SRVC method.} + +\item{BCmethod}{Specification of the biclustering method, +including 'BCBimax', 'BCCC', 'BCPlaid' (default), 'BCQuest', +'BCSpectral', 'BCXmotifs'. Only for the SM method.} + +\item{CRC_method}{the method of calculating matrix correlation. Select +one of 'Coxhead' and 'Rozeboom' methods. +Only for the SCRC method.} +} +\value{ +List object: Group competition of miRNA sponge modules, +and miRNA sponge modules. +} +\description{ +Identify miRNA sponge modules using sensitivity canonical correlation (SCC), +sensitivity distance correlation (SDC), +sensitivity RV coefficient (SRVC), sensitivity similarity index (SSI), +sensitivity generalized coefficient of determination (SGCD), +sensitivity Coxhead's or Rozeboom's coefficient (SCRC), +and sponge module (SM) methods. +} +\examples{ +data(BRCASampleData) +modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)], + mRExp[, seq_len(10)]) +# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) +miRSM_igraph_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, + modulegenes_igraph, method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV") + +} +\references{ +Witten DM, Tibshirani R, Hastie T. A penalized matrix +decomposition, with applications to sparse principal components +and canonical correlation analysis. Biostatistics. +2009, 10(3):515-34. + +Szekely GJ, Rizzo ML. Partial distance +correlation with methods for dissimilarities. Annals of Statistics. +2014, 42(6):2382-2412. + +Szekely GJ, Rizzo ML, Bakirov NK. +Measuring and Testing Dependence by Correlation of Distances, +Annals of Statistics, 2007, 35(6):2769-2794. + +Robert P, Escoufier Y. A unifying tool for +linear multivariate statistical methods: the RV-Coefficient. +Applied Statistics, 1976, 25(3):257-265. + +Smilde AK, Kiers HA, Bijlsma S, Rubingh CM, +van Erk MJ. Matrix correlations for high-dimensional +data: the modified RV-coefficient. Bioinformatics, +2009, 25(3):401-405. + +Maye CD, Lorent J, Horgan GW. +Exploratory analysis of multiple omics datasets using +the adjusted RV coefficient". Stat Appl Genet Mol Biol., +2011, 10, 14. + +EIGhaziri A, Qannari EM. Measures +of association between two datasets; Application to sensory data, +Food Quality and Preference, 2015, 40(A):116-124. + +Indahl UG, Næs T, Liland KH. A similarity index for +comparing coupled matrices. Journal of Chemometrics. 2018; 32:e3049. + +Yanai H. Unification of various techniques of multivariate +analysis by means of generalized coefficient of determination (GCD). +Journal of Behaviormetrics, 1974, 1(1): 45-54. + +Coxhead P. Measuring the relationship between two sets +of variables. British journal of mathematical and statistical psychology, +1974, 27(2): 205-212. + +Rozeboom WW. Linear correlations between sets of variables. +Psychometrika, 1965, 30(1): 57-71. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/miRSM_SS.Rd b/man/miRSM_SS.Rd new file mode 100644 index 0000000..2945129 --- /dev/null +++ b/man/miRSM_SS.Rd @@ -0,0 +1,56 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{miRSM_SS} +\alias{miRSM_SS} +\title{miRSM_SS} +\usage{ +miRSM_SS( + Modulelist.all, + Modulelist.exceptk, + sim.cutoff = 0.8, + sim.method = "Simpson" +) +} +\arguments{ +\item{Modulelist.all}{List object, modules using all of samples.} + +\item{Modulelist.exceptk}{List object, modules using all of samples excepting sample k.} + +\item{sim.cutoff}{Similarity cutoff between modules, the interval is [0 1].} + +\item{sim.method}{Methods for calculating similatiry between two modules, select one of three methods (Simpson, Jaccard and Lin). Default method is Simpson.} +} +\value{ +A list of sample-specific miRNA sponge modules +} +\description{ +Inferring sample-specific miRNA sponge modules +} +\examples{ +data(BRCASampleData) +nsamples <- 3 +modulegenes_igraph_all <- module_igraph(ceRExp[, 151:300], mRExp[, 151:300]) +modulegenes_WGCNA_exceptk <- lapply(seq(nsamples), function(i) + module_WGCNA(ceRExp[-i, seq(150)], + mRExp[-i, seq(150)])) + +miRSM_igraph_SRVC_all <- miRSM(miRExp, ceRExp[, 151:300], mRExp[, 151:300], + miRTarget, modulegenes_igraph_all, + method = "SRVC", SMC.cutoff = 0.01, + RV_method = "RV") +miRSM_WGCNA_SRVC_exceptk <- lapply(seq(nsamples), function(i) miRSM(miRExp[-i, ], + ceRExp[-i, seq(150)], mRExp[-i, seq(150)], + miRTarget, modulegenes_WGCNA_exceptk[[i]],#' + method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV")) + +Modulegenes_all <- miRSM_igraph_SRVC_all[[2]] +Modulegenes_exceptk <- lapply(seq(nsamples), function(i) + miRSM_WGCNA_SRVC_exceptk[[i]][[2]]) + +Modules_SS <- miRSM_SS(Modulegenes_all, Modulegenes_exceptk) + +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/miRTarget.Rd b/man/miRTarget.Rd new file mode 100644 index 0000000..cae6ae7 --- /dev/null +++ b/man/miRTarget.Rd @@ -0,0 +1,32 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{miRTarget} +\alias{miRTarget} +\title{miRNA-target ineractions} +\format{ +miRTarget: A SummarizedExperiment object with +29901 miRNA-target interactions. +} +\description{ +miRNA-target ineractions +} +\details{ +The miRNA-target binding information is +from miRTarBase v8.0 (http://mirtarbase.mbc.nctu.edu.tw/php/index.php), +and LncBase v2.0 +(http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2/index). +Among 226 miRNAs, 305 lncRNAs and 500 mRNAs +which are differentially expressed, we obtain 29901 miRNA-target +interactions (including miRNA-lncRNA and miRNA-mRNA interactions). +} +\references{ +Hastie T, Tibshirani R, Narasimhan B, Chu G. +impute: Imputation for microarray data. +R package version 1.54.0. doi: 10.18129/B9.bioc.impute. + +Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, +Shi W, et al. limma powers differential expression +analyses for RNA-sequencing and microarray studies. +Nucleic Acids Res. 2015; 43(7):e47. +} diff --git a/man/module_CEA.Rd b/man/module_CEA.Rd new file mode 100644 index 0000000..90bc8f6 --- /dev/null +++ b/man/module_CEA.Rd @@ -0,0 +1,44 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_CEA} +\alias{module_CEA} +\title{module_CEA} +\usage{ +module_CEA(ceRExp, mRExp = NULL, Cancergenes, Modulelist) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{Cancergenes}{A SummarizedExperiment object: a list of cancer genes given.} + +\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} +} +\value{ +Cancer enrichment significance p-values of the identified miRNA sponge modules +} +\description{ +Cancer enrichment analysis of miRNA sponge modules using hypergeometric distribution test +} +\examples{ +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) +# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) +miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, + modulegenes_WGCNA, method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV") +miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] +miRSM.CEA.pvalue <- module_CEA(ceRExp, mRExp, BRCA_genes, + miRSM_WGCNA_SRVC_genes) + +} +\references{ +Johnson NL, Kotz S, Kemp AW (1992) +"Univariate Discrete Distributions", Second Edition. New York: Wiley. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_Coexpress.Rd b/man/module_Coexpress.Rd new file mode 100644 index 0000000..aa43181 --- /dev/null +++ b/man/module_Coexpress.Rd @@ -0,0 +1,59 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_Coexpress} +\alias{module_Coexpress} +\title{module_Coexpress} +\usage{ +module_Coexpress( + ceRExp, + mRExp = NULL, + Modulelist, + resample = 1000, + method = c("mean", "median"), + test.method = c("t.test", "wilcox.test") +) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} + +\item{resample}{The number of random miRNA sponge modules generated, and 1000 times in default.} + +\item{method}{The method used to evaluate the co-expression level of each miRNA sponge module. +Users can select "mean" or "median" to calculate co-expression value of each miRNA sponge module +and its corresponding random miRNA sponge module.} + +\item{test.method}{The method used to evaluate statistical significance p-value of +co-expression level higher than random miRNA sponge modules. +Users can select "t.test" or "wilcox.test" to calculate statistical significance p-value of +co-expression level higher than random miRNA sponge modules.} +} +\value{ +List object: co-expression values of miRNA sponge modules and their corresponding random miRNA sponge modules, +and statistical significance p-value of co-expression level higher than random miRNA sponge modules. +} +\description{ +Co-expression analysis of each miRNA sponge module and its corresponding random miRNA sponge modules +} +\examples{ +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) +# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) +miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, + modulegenes_WGCNA, method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV") +miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] +miRSM_WGCNA_Coexpress <- module_Coexpress(ceRExp, mRExp, + miRSM_WGCNA_SRVC_genes, + resample = 10, method = "mean", + test.method = "t.test") + +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_FA.Rd b/man/module_FA.Rd new file mode 100644 index 0000000..3a7c2d5 --- /dev/null +++ b/man/module_FA.Rd @@ -0,0 +1,80 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_FA} +\alias{module_FA} +\title{module_FA} +\usage{ +module_FA( + Modulelist, + GOont = "BP", + Diseaseont = "DO", + KEGGorganism = "hsa", + Reactomeorganism = "human", + OrgDb = "org.Hs.eg.db", + padjustvaluecutoff = 0.05, + padjustedmethod = "BH", + Analysis.type = c("FEA", "DEA") +) +} +\arguments{ +\item{Modulelist}{List object: a list of miRNA sponge modules.} + +\item{GOont}{One of 'MF', 'BP', and 'CC' subontologies.} + +\item{Diseaseont}{One of 'DO', and 'DOLite' subontologies.} + +\item{KEGGorganism}{Organism, supported organism listed +in http://www.genome.jp/kegg/catalog/org_list.html.} + +\item{Reactomeorganism}{Organism, one of 'human', 'rat', ' +mouse', 'celegans', 'yeast', 'zebrafish', 'fly'.} + +\item{OrgDb}{OrgDb} + +\item{padjustvaluecutoff}{A cutoff value of adjusted p-values.} + +\item{padjustedmethod}{Adjusted method of p-values, can select +one of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', +'fdr', 'none'.} + +\item{Analysis.type}{The type of functional analysis selected, +including 'FEA' (functional enrichment analysis) and 'DEA' +(disease enrichment analysis).} +} +\value{ +List object: a list of enrichment analysis results. +} +\description{ +Functional analysis of miRNA sponge modules, including functional +enrichment and disease enrichment analysis +} +\examples{ +\dontrun{ +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) +# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) +miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, + modulegenes_WGCNA, method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV") +miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] +miRSM_WGCNA_SRVC_FEA <- module_FA(miRSM_WGCNA_SRVC_genes, Analysis.type = 'FEA') +miRSM_WGCNA_SRVC_DEA <- module_FA(miRSM_WGCNA_SRVC_genes, Analysis.type = 'DEA') +} + +} +\references{ +Zhang J, Liu L, Xu T, Xie Y, Zhao C, Li J, Le TD (2019). +“miRspongeR: an R/Bioconductor package for the identification and analysis of +miRNA sponge interaction networks and modules.” BMC Bioinformatics, 20, 235. + +Zhang J, Liu L, Zhang W, Li X, Zhao C, Li S, Li J, Le TD. +miRspongeR 2.0: an enhanced R package for exploring miRNA sponge regulation. +Bioinform Adv. 2022 Sep 2;2(1):vbac063. + +Yu G, Wang L, Han Y, He Q (2012). +“clusterProfiler: an R package for comparing biological themes among gene clusters.” +OMICS: A Journal of Integrative Biology, 16(5), 284-287. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_GFA.Rd b/man/module_GFA.Rd new file mode 100644 index 0000000..8e1816d --- /dev/null +++ b/man/module_GFA.Rd @@ -0,0 +1,56 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_GFA} +\alias{module_GFA} +\title{module_GFA} +\usage{ +module_GFA( + ceRExp, + mRExp = NULL, + StrengthCut = 0.9, + iter.max = 5000, + num.ModuleceRs = 2, + num.ModulemRs = 2 +) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{StrengthCut}{Desired minimum strength (absolute value of +association with interval [0 1]) for each bicluster.} + +\item{iter.max}{The total number of Gibbs sampling steps +(default 1000).} + +\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} + +\item{num.ModulemRs}{The minimum number of mRNAs in each module.} +} +\value{ +GeneSetCollection object: a list of module genes. +} +\description{ +Identification of gene modules from matched ceRNA and mRNA +expression data using GFA package +} +\examples{ +data(BRCASampleData) +modulegenes_GFA <- module_GFA(ceRExp[seq_len(20), seq_len(15)], + mRExp[seq_len(20), seq_len(15)], iter.max = 2600) + +} +\references{ +Bunte K, Lepp\'{a}aho E, Saarinen I, Kaski S. +Sparse group factor analysis for biclustering of multiple data sources. Bioinformatics. 2016, 32(16):2457-63. + +Lepp\'{a}aho E, Ammad-ud-din M, Kaski S. GFA: +exploratory analysis of multiple data sources with group factor +analysis. J Mach Learn Res. 2017, 18(39):1-5. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_NMF.Rd b/man/module_NMF.Rd new file mode 100644 index 0000000..5ba1eda --- /dev/null +++ b/man/module_NMF.Rd @@ -0,0 +1,54 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_NMF} +\alias{module_NMF} +\title{module_NMF} +\usage{ +module_NMF( + ceRExp, + mRExp = NULL, + NMF.algorithm = "brunet", + num.modules = 10, + num.ModuleceRs = 2, + num.ModulemRs = 2 +) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{NMF.algorithm}{Specification of the NMF algorithm, +including 'brunet' (default), 'Frobenius', 'KL', 'lee', 'nsNMF', +'offset', 'siNMF', 'snmf/l', 'snmf/r'.} + +\item{num.modules}{The number of modules to be identified.} + +\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} + +\item{num.ModulemRs}{The minimum number of mRNAs in each module.} +} +\value{ +GeneSetCollection object: a list of module genes. +} +\description{ +Identification of gene modules from matched ceRNA and mRNA +expression data using NMF package +} +\examples{ +data(BRCASampleData) +# Reimport NMF package to avoid conflicts with DelayedArray package +library(NMF) +modulegenes_NMF <- module_NMF(ceRExp[, seq_len(10)], + mRExp[, seq_len(10)]) + +} +\references{ +Gaujoux R, Seoighe C. A flexible R package for +nonnegative matrix factorization. BMC Bioinformatics. 2010, 11:367. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_ProNet.Rd b/man/module_ProNet.Rd new file mode 100644 index 0000000..c762b95 --- /dev/null +++ b/man/module_ProNet.Rd @@ -0,0 +1,71 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_ProNet} +\alias{module_ProNet} +\title{module_ProNet} +\usage{ +module_ProNet( + ceRExp, + mRExp = NULL, + cor.method = "pearson", + pos.p.value.cutoff = 0.01, + cluster.method = "MCL", + num.ModuleceRs = 2, + num.ModulemRs = 2 +) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{cor.method}{The method of calculating correlation selected, +including 'pearson' (default), 'kendall', 'spearman'.} + +\item{pos.p.value.cutoff}{The significant p-value cutoff of +positive correlation} + +\item{cluster.method}{The clustering method selected in +\pkg{ProNet} package, including 'FN', 'MCL' (default), +'LINKCOMM', 'MCODE'.} + +\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} + +\item{num.ModulemRs}{The minimum number of mRNAs in each module.} +} +\value{ +GeneSetCollection object: a list of module genes. +} +\description{ +Identification of gene modules from matched ceRNA and mRNA +expression data using ProNet package +} +\examples{ +data(BRCASampleData) +modulegenes_ProNet <- module_ProNet(ceRExp[, seq_len(10)], + mRExp[, seq_len(10)]) + +} +\references{ +Clauset A, Newman ME, Moore C. Finding community +structure in very large networks. Phys Rev E Stat Nonlin Soft +Matter Phys., 2004, 70(6 Pt 2):066111. + +Enright AJ, Van Dongen S, Ouzounis CA. An efficient +algorithm for large-scale detection of protein families. +Nucleic Acids Res., 2002, 30(7):1575-84. + +Kalinka AT, Tomancak P. linkcomm: an R package +for the generation, visualization, and analysis of link +communities in networks of arbitrary size and type. +Bioinformatics, 2011, 27(14):2011-2. + +Bader GD, Hogue CW. An automated method for +finding molecular complexes in large protein interaction +networks. BMC Bioinformatics, 2003, 4:2. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_Validate.Rd b/man/module_Validate.Rd new file mode 100644 index 0000000..c0dbaf7 --- /dev/null +++ b/man/module_Validate.Rd @@ -0,0 +1,35 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_Validate} +\alias{module_Validate} +\title{module_Validate} +\usage{ +module_Validate(Modulelist, Groundtruth) +} +\arguments{ +\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} + +\item{Groundtruth}{Matrix object: a list of experimentally validated miRNA sponge interactions.} +} +\value{ +List object: a list of validated miRNA sponge interactions in each miRNA sponge module +} +\description{ +Validation of miRNA sponge interactions in each miRNA sponge module +} +\examples{ +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) +# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) +miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, + modulegenes_WGCNA, method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV") +miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] +Groundtruthcsv <- system.file("extdata", "Groundtruth.csv", package="miRSM") +Groundtruth <- read.csv(Groundtruthcsv, header=TRUE, sep=",") +miRSM.Validate <- module_Validate(miRSM_WGCNA_SRVC_genes, Groundtruth) + +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_WGCNA.Rd b/man/module_WGCNA.Rd new file mode 100644 index 0000000..23ff8bd --- /dev/null +++ b/man/module_WGCNA.Rd @@ -0,0 +1,48 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_WGCNA} +\alias{module_WGCNA} +\title{module_WGCNA} +\usage{ +module_WGCNA( + ceRExp, + mRExp = NULL, + RsquaredCut = 0.9, + num.ModuleceRs = 2, + num.ModulemRs = 2 +) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{RsquaredCut}{Desired minimum scale free topology fitting index +R^2 with interval [0 1].} + +\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} + +\item{num.ModulemRs}{The minimum number of mRNAs in each module.} +} +\value{ +GeneSetCollection object: a list of module genes. +} +\description{ +Identification of co-expressed gene modules from matched ceRNA and mRNA +expression data using WGCNA package +} +\examples{ +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp[, seq_len(80)], + mRExp[, seq_len(80)]) + +} +\references{ +Langfelder P, Horvath S. WGCNA: an R package for weighted +correlation network analysis. BMC Bioinformatics. 2008, 9:559.#' +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_biclust.Rd b/man/module_biclust.Rd new file mode 100644 index 0000000..23defcf --- /dev/null +++ b/man/module_biclust.Rd @@ -0,0 +1,112 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_biclust} +\alias{module_biclust} +\title{module_biclust} +\usage{ +module_biclust( + ceRExp, + mRExp = NULL, + BCmethod = "fabia", + num.modules = 10, + num.ModuleceRs = 2, + num.ModulemRs = 2 +) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{BCmethod}{Specification of the biclustering method, +including 'BCBimax', 'BCCC', 'BCPlaid' (default), 'BCQuest', +'BCSpectral', 'BCXmotifs', iBBiG', 'fabia', 'fabiap', +'fabias', 'mfsc', 'nmfdiv', 'nmfeu', 'nmfsc', 'FLOC', 'isa', +'BCs4vd', 'BCssvd', 'bibit' and 'quBicluster'.} + +\item{num.modules}{The number of modules to be identified. For the 'BCPlaid', +'BCSpectral', 'isa' and 'bibit' methods, no need to set the parameter. For the +'quBicluster' method, the parameter is used to set the number of biclusters +that should be reported.} + +\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} + +\item{num.ModulemRs}{The minimum number of mRNAs in each module.} +} +\value{ +GeneSetCollection object: a list of module genes. +} +\description{ +Identification of gene modules from matched ceRNA and mRNA +expression data using a series of biclustering packages, +including biclust, iBBiG, fabia, BicARE, isa2, s4vd, +BiBitR and rqubic +} +\examples{ +data(BRCASampleData) +modulegenes_biclust <- module_biclust(ceRExp[, seq_len(30)], + mRExp[, seq_len(30)]) + +} +\references{ +Preli\'{c} A, Bleuler S, Zimmermann P, Wille A, +B\'{u}hlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E. +A systematic comparison and evaluation of biclustering methods +for gene expression data. Bioinformatics. 2006, 22(9):1122-9. + +Cheng Y, Church GM. Biclustering of expression data. +Proc Int Conf Intell Syst Mol Biol. 2000, 8:93-103. + +Turner H, Bailey T, Krzanowski W. Improved +biclustering of microarray data demonstrated through systematic +performance tests. Comput Stat Data Anal. 2003, 48(2): 235-254. + +Murali TM, Kasif S. Extracting conserved gene +expression motifs from gene expression data. +Pac Symp Biocomput. 2003:77-88. + +Kluger Y, Basri R, Chang JT, Gerstein M. +Spectral biclustering of microarray data: coclustering genes +and conditions. Genome Res. 2003, 13(4):703-16. + +Gusenleitner D, Howe EA, Bentink S, Quackenbush J, +Culhane AC. iBBiG: iterative binary bi-clustering of gene sets. +Bioinformatics. 2012, 28(19):2484-92. + +Hochreiter S, Bodenhofer U, Heusel M, Mayr A, +Mitterecker A, Kasim A, Khamiakova T, Van Sanden S, Lin D, +Talloen W, Bijnens L, G\'{o}hlmann HW, Shkedy Z, Clevert DA. +FABIA: factor analysis for bicluster acquisition. +Bioinformatics. 2010, 26(12):1520-7. + +Yang J, Wang H, Wang W, Yu, PS. An improved +biclustering method for analyzing gene expression. +Int J Artif Intell Tools. 2005, 14(5): 771-789. + +Bergmann S, Ihmels J, Barkai N. Iterative +signature algorithm for the analysis of large-scale gene +expression data. Phys Rev E Stat Nonlin Soft Matter Phys. +2003, 67(3 Pt 1):031902. + +Sill M, Kaiser S, Benner A, Kopp-Schneider A. +Robust biclustering by sparse singular value decomposition +incorporating stability selection. Bioinformatics. 2011, +27(15):2089-97. + +Lee M, Shen H, Huang JZ, Marron JS. Biclustering +via sparse singular value decomposition. Biometrics. 2010, +66(4):1087-95. + +Rodriguez-Baena DS, Perez-Pulido AJ, Aguilar-Ruiz JS. +A biclustering algorithm for extracting bit-patterns from +binary datasets. Bioinformatics. 2011, 27(19):2738-45. + +Li G, Ma Q, Tang H, Paterson AH, Xu Y. +QUBIC: a qualitative biclustering algorithm for analyses of +gene expression data. Nucleic Acids Res. 2009, 37(15):e101. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_clust.Rd b/man/module_clust.Rd new file mode 100644 index 0000000..2875caf --- /dev/null +++ b/man/module_clust.Rd @@ -0,0 +1,106 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_clust} +\alias{module_clust} +\title{module_clust} +\usage{ +module_clust( + ceRExp, + mRExp = NULL, + cluster.method = "kmeans", + num.modules = 10, + num.ModuleceRs = 2, + num.ModulemRs = 2 +) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{cluster.method}{Specification of the clustering method, +including 'kmeans'(default), 'hclust', 'dbscan' , 'clique', +'gmm', 'som' and 'fcm'.} + +\item{num.modules}{Parameter of the number of modules to be identified +for the 'kmeans', 'hclust', 'gmm' and 'fcm' methods. Parameter of the number +of intervals for the 'clique' method. For the 'dbscan' and 'som' methods, +no need to set the parameter.} + +\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} + +\item{num.ModulemRs}{The minimum number of mRNAs in each module.} +} +\value{ +GeneSetCollection object: a list of module genes. +} +\description{ +Identification of gene modules from matched ceRNA and mRNA +expression data using a series of clustering packages, +including stats, flashClust, dbscan, subspace, mclust, SOMbrero and ppclust packages. +} +\examples{ +data(BRCASampleData) +modulegenes_clust <- module_clust(ceRExp[, seq_len(30)], + mRExp[, seq_len(30)]) + +} +\references{ +Forgy EW. Cluster analysis of multivariate +data: efficiency vs interpretability of classifications. +Biometrics, 1965, 21:768-769. + +Hartigan JA, Wong MA. +Algorithm AS 136: A K-means clustering algorithm. +Applied Statistics, 1979, 28:100-108. + +Lloyd SP. Least squares quantization in PCM. +Technical Note, Bell Laboratories. Published in 1982 +in IEEE Transactions on Information Theory, 1982, 28:128-137. + +MacQueen J. Some methods for classification +and analysis of multivariate observations. +In Proceedings of the Fifth Berkeley Symposium on +Mathematical Statistics and Probability, +eds L. M. Le Cam & J. Neyman, 1967, 1, pp.281-297. +Berkeley, CA: University of California Press. + +Langfelder P, Horvath S. Fast R Functions for +Robust Correlations and Hierarchical Clustering. +Journal of Statistical Software. 2012, 46(11):1-17. + +Ester M, Kriegel HP, Sander J, Xu X. A density-based +algorithm for discovering clusters in large spatial databases with +noise, Proceedings of 2nd International Conference on Knowledge Discovery and +Data Mining (KDD-96), 1996, 96(34): 226-231. + +Campello RJGB, Moulavi D, Sander J. +Density-based clustering based on hierarchical density estimates, +Pacific-Asia conference on knowledge discovery and data mining. +Springer, Berlin, Heidelberg, 2013: 160-172. + +Agrawal R, Gehrke J, Gunopulos D, Raghavan P. +Automatic subspace clustering of high dimensional data for +data mining applications. In Proc. ACM SIGMOD, 1998. + +Scrucca L, Fop M, Murphy TB, Raftery AE. +mclust 5: clustering, classification and density estimation using +Gaussian finite mixture models The R Journal 8/1, 2016, pp. 205-233. + +Kohonen T. Self-Organizing Maps. +Berlin/Heidelberg: Springer-Verlag, 3rd edition, 2001. + +Dunn JC. A fuzzy relative of the ISODATA process +and its use in detecting compact well-separated clusters. Journal of Cybernetics, +1973, 3(3):32-57. + +Bezdek JC. Cluster validity with fuzzy sets. Journal of Cybernetics, 1974, 3: 58-73. + +Bezdek JC. Pattern recognition with fuzzy objective function +algorithms. Plenum, NY, 1981. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_group_sim.Rd b/man/module_group_sim.Rd new file mode 100644 index 0000000..c988f19 --- /dev/null +++ b/man/module_group_sim.Rd @@ -0,0 +1,39 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_group_sim} +\alias{module_group_sim} +\title{module_group_sim} +\usage{ +module_group_sim(Module.group1, Module.group2, sim.method = "Simpson") +} +\arguments{ +\item{Module.group1}{List object, the first list of module group.} + +\item{Module.group2}{List object, the second list of module group.} + +\item{sim.method}{Methods for calculating similatiry between two modules, select one of three methods (Simpson, Jaccard and Lin). Default method is Simpson.} +} +\value{ +Similarity between two list of module groups +} +\description{ +Calculating similarity between two list of module groups +} +\examples{ +library(GSEABase) +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) +modulegenes_igraph <- module_igraph (ceRExp, mRExp) +Sim <- module_group_sim(geneIds(modulegenes_WGCNA), geneIds(modulegenes_igraph)) + +} +\references{ +Simpson E H. Measurement of diversity. Nature, 1949, 163(4148): 688-688. + +Jaccard P. The distribution of the flora in the alpine zone. 1. New phytologist, 1912, 11(2): 37-50. + +Lin D. An information-theoretic definition of similarity. in: Icml. 1998, 98(1998): 296-304. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_igraph.Rd b/man/module_igraph.Rd new file mode 100644 index 0000000..949e2e2 --- /dev/null +++ b/man/module_igraph.Rd @@ -0,0 +1,57 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_igraph} +\alias{module_igraph} +\title{module_igraph} +\usage{ +module_igraph( + ceRExp, + mRExp = NULL, + cor.method = "pearson", + pos.p.value.cutoff = 0.01, + cluster.method = "greedy", + num.ModuleceRs = 2, + num.ModulemRs = 2 +) +} +\arguments{ +\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: +rows are samples and columns are ceRNAs.} + +\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: +rows are samples and columns are mRNAs.} + +\item{cor.method}{The method of calculating correlation selected, +including 'pearson' (default), 'kendall', 'spearman'.} + +\item{pos.p.value.cutoff}{The significant p-value cutoff of +positive correlation.} + +\item{cluster.method}{The clustering method selected in +\pkg{igraph} package, including 'betweenness', 'greedy' (default), +'infomap', 'prop', 'eigen', 'louvain', 'walktrap'.} + +\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.} + +\item{num.ModulemRs}{The minimum number of mRNAs in each module.} +} +\value{ +GeneSetCollection object: a list of module genes. +} +\description{ +Identification of gene modules from matched ceRNA and mRNA +expression data using igraph package +} +\examples{ +data(BRCASampleData) +modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)], + mRExp[, seq_len(10)]) + +} +\references{ +Csardi G, Nepusz T. The igraph software package for +complex network research, InterJournal, Complex Systems. 2006:1695. +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_miRdistribute.Rd b/man/module_miRdistribute.Rd new file mode 100644 index 0000000..5dd275c --- /dev/null +++ b/man/module_miRdistribute.Rd @@ -0,0 +1,33 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_miRdistribute} +\alias{module_miRdistribute} +\title{module_miRdistribute} +\usage{ +module_miRdistribute(share_miRs) +} +\arguments{ +\item{share_miRs}{List object: a list of common miRNAs of each miRNA sponge module +generated by share_miRs function.} +} +\value{ +Matrix object: miRNA distribution in each miRNA sponge module. +} +\description{ +miRNA distribution analysis of sharing miRNAs by the identified miRNA sponge modules +} +\examples{ +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) +# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) +miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, + modulegenes_WGCNA, method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV") +miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] +miRSM_WGCNA_share_miRs <- share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes) +miRSM_WGCNA_miRdistribute <- module_miRdistribute(miRSM_WGCNA_share_miRs) + +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_miRsponge.Rd b/man/module_miRsponge.Rd new file mode 100644 index 0000000..650f190 --- /dev/null +++ b/man/module_miRsponge.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_miRsponge} +\alias{module_miRsponge} +\title{module_miRsponge} +\usage{ +module_miRsponge(Modulelist) +} +\arguments{ +\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} +} +\value{ +List object: miRNA sponge interactions of each miRNA sponge module. +} +\description{ +Extract miRNA sponge interactions of each miRNA sponge module +} +\examples{ +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) +# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) +miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, + modulegenes_WGCNA, method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV") +miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] +miRSM_WGCNA_miRsponge <- module_miRsponge(miRSM_WGCNA_SRVC_genes) + +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/module_miRtarget.Rd b/man/module_miRtarget.Rd new file mode 100644 index 0000000..3757cab --- /dev/null +++ b/man/module_miRtarget.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{module_miRtarget} +\alias{module_miRtarget} +\title{module_miRtarget} +\usage{ +module_miRtarget(share_miRs, Modulelist) +} +\arguments{ +\item{share_miRs}{List object: a list of common miRNAs of each miRNA sponge module +generated by share_miRs function.} + +\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} +} +\value{ +List object: miRNA-target interactions of each miRNA sponge module. +} +\description{ +Extract miRNA-target interactions of each miRNA sponge module +} +\examples{ +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) +# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) +miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, + modulegenes_WGCNA, method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV") +miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] +miRSM_WGCNA_share_miRs <- share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes) +miRSM_WGCNA_miRtarget <- module_miRtarget(miRSM_WGCNA_share_miRs, + miRSM_WGCNA_SRVC_genes) + +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +} diff --git a/man/share_miRs.Rd b/man/share_miRs.Rd new file mode 100644 index 0000000..3420d89 --- /dev/null +++ b/man/share_miRs.Rd @@ -0,0 +1,34 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/miRSM.R +\name{share_miRs} +\alias{share_miRs} +\title{share_miRs} +\usage{ +share_miRs(miRTarget, Modulelist) +} +\arguments{ +\item{miRTarget}{A SummarizedExperiment object. Putative +miRNA-target binding information.} + +\item{Modulelist}{List object: a list of the identified miRNA sponge modules.} +} +\value{ +List object: a list of common miRNAs of each miRNA sponge module. +} +\description{ +Extract common miRNAs of each miRNA sponge module +} +\examples{ +data(BRCASampleData) +modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) +# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC) +miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, + modulegenes_WGCNA, method = "SRVC", + SMC.cutoff = 0.01, RV_method = "RV") +miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] +miRSM_WGCNA_share_miRs <- share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes) + +} +\author{ +Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2}) +}