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differentially methylated regions (DMR)

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@marcmaxson marcmaxson released this 19 Oct 22:07
· 11 commits to master since this release
v0.9.9
757059a
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This version now has a complete pipeline for running EWAS, with DMR and DMP functions.

What's Changed since last release

  • Added a differentially methylated regions (DMR) functions that takes the output of the diff_meth_pos (DMP) function.
    • DMP maps differences to chromosomes; DMR maps differences to specific genomic locii, and requires more processing.
    • upgraded methylprep manifests to support both old and new genomic build mappings for all array types.
      In general, you can supply a keyword argument (genome_build='OLD') to change from the new build back to the old one.
    • Genome annotation. But won't work with mouse array.
    • DMP integrates the combined-pvalues package (https://pubmed.ncbi.nlm.nih.gov/22954632/)
    • DMP integrates with UCSC Genome (refGene) and annotates the genes near CpG regions.
    • Annotation includes column(s) showing the tissue specific expression levels of relevant genes (e.g. filter=blood)
  • to_BED provides output BED for export to other genomic analysis tools
  • fixed methylize.diff_meth_pos linear regression. upgraded features too
    • Support for including/excluding sex chromosomes from DMP (probe2chr map)
  • dotted manhattan_plot sig line is Bonferoni corrected (pass in post_test=None to leave uncorrected)
    • probes sorted by MAPINFO (chromosome location) instead of FDR_QValue on manhattan plots now
  • better test coverage in general

Full Changelog: v0.9.0...v0.9.9

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