Data file format

[vdvornyk1]

Dear Florian,

I am trying to use your bigsnpr package for R but I puzzled with the data format. Could you explain it for dummy and give respective examples?

Thank you.

Best,

Volodymyr

[privefl]

You're right, documentation could probably be better on this.
But, could you be a bit more precise on what part is puzzling you?

Is this helping?

• https://privefl.github.io/bigsnpr-extdoc/inputs-and-formats.html#inputs-and-formats
• https://privefl.github.io/bigstatsr/reference/FBM.code256-class.html#examples
• https://privefl.github.io/bigsnpr/reference/bigSNP-class.html

[vdvornyk1]

The links you have provided help but not much. You need to understand that most users of your software (like me) are not R experts. Therefore, the instructions should be as simple as possible. Otherwise, I have to spend days or weeks trying to figure out how to use your software. Specifically, you give three examples: X <- FBM(10, 10, type = "raw") X[] <- sample(as.raw(0:3), size = length(X), replace = TRUE) X[] #> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] #> [1,] 03 00 01 02 01 02 03 01 03 03 #> [2,] 01 03 00 01 00 03 01 02 01 03 #> [3,] 01 03 00 00 01 01 03 00 01 03 #> [4,] 03 01 02 02 03 00 01 00 00 02 #> [5,] 03 01 02 03 00 01 00 00 02 00 #> [6,] 01 03 03 01 03 02 00 00 02 03 #> [7,] 01 01 02 02 00 01 00 02 00 02 #> [8,] 02 00 01 00 03 03 02 00 02 00 #> [9,] 03 00 01 00 00 01 03 01 00 01 #> [10,] 00 00 02 03 00 01 02 00 03 02 # From an FBM of type 'raw' ('unsigned char') code <- rep(NA_real_, 256) code[1:3] <- c(1, 3, 5) X.code <- add_code256(X, code) X.code[] #> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] #> [1,] NA 1 3 5 3 5 NA 3 NA NA #> [2,] 3 NA 1 3 1 NA 3 5 3 NA #> [3,] 3 NA 1 1 3 3 NA 1 3 NA #> [4,] NA 3 5 5 NA 1 3 1 1 5 #> [5,] NA 3 5 NA 1 3 1 1 5 1 #> [6,] 3 NA NA 3 NA 5 1 1 5 NA #> [7,] 3 3 5 5 1 3 1 5 1 5 #> [8,] 5 1 3 1 NA NA 5 1 5 1 #> [9,] NA 1 3 1 1 3 NA 3 1 3 #> [10,] 1 1 5 NA 1 3 5 1 NA 5 # Or directly X.code2 <- FBM.code256(10, 10, code, init = sample(as.raw(0:3), 100, TRUE)) X.code2[] #> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] #> [1,] 1 3 3 NA 3 5 1 NA 5 3 #> [2,] 5 5 3 NA 3 NA 5 5 1 NA #> [3,] 1 NA 1 1 NA NA 3 1 1 3 #> [4,] 5 NA 1 5 1 5 1 1 3 1 #> [5,] 5 1 3 NA NA 1 3 5 5 3 #> [6,] 5 5 NA NA 1 1 5 5 5 NA #> [7,] 3 1 1 NA NA 3 3 1 5 1 #> [8,] NA 3 NA 1 NA 1 1 NA 3 NA #> [9,] 3 NA NA 3 5 3 5 NA 3 5 #> [10,] NA NA 1 5 3 NA NA 3 1 3 # Get a new FBM.code256 object with another code (but same underlying data) X.code3 <- X.code$copy(code = rnorm(256)) all.equal(X.code$code256, code) #> [1] TRUE Which one should be used in what case? What are the values [1,], [2,], and [,1], [,2], etc.? What are these codes: X.code2 <- FBM.code256(10, 10, code, init = sample(as.raw(0:3), 100, TRUE)) X.code2[]? Should they be included in the data file? More questions than answers.] I have a data file like this: Sample (Male/Female/Unknown) rs12608932 rs302668 HG01879 (M) A A T C HG01880 (F) C C T C HG01882 (M) C A T T HG01883 (F) A C T C HG01885 (M) A A T T HG01886 (F) C A T T HG01889 (F) A C T T HG01890 (M) C A T T How can I transform it into a the data file format for your software? What else is needed for the analysis? Best, Volodymyr

[privefl]

The packages are made for people that want to do most of their genetic analyses within R; usually people with some experience in R.
If you are not familiar with standard matrix accessors in R, it might be complicated for you to use the packages, sorry.

With such data format that you have (does it have a name ?), usually you can use PLINK to convert to bed/bim/fam, and then use snp_readBed/2() to convert to my format.