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DMRichR v1.5.0
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@ben-laufer ben-laufer released this 20 Sep 16:55
· 33 commits to master since this release
v1.5.0
bb67ddd

New Features:

  • The DMRichment family of functions has been added and serves as an homage to the one of the original goals of DMRichR. DMRichCpG() and DMRichGenic() test for signficant enrichments of the DMRs (relative to background regions) within CpG and gene region (genic) annotations via a Fisher's exact test with FDR correction. DMRichPlot() plots the results of both types of enrichment tests and DMparseR() can be used to create a DMRichPlot() with facets for all DMRs, hypermethylated DMRs, and hypomethylated DMRs. Finally, imprintOverlap() tests for enrichments within human imprinted genes.
  • singleCpGPCA() has been introduced.
  • Added the maxBlockPerms option to DM.R. Default is 10.

Improvements:

  • Added CpG island statistics to globalStats() for hg38, hg19, mm10, mm9, rn6.
  • REVIGO() has been parsed from GOplot() so that the full list of slimmed gene ontologies can be saved. This also enables use with other pipelines that utilize GREAT, GOfuncR or enrichr.
  • Added average length and average number of CpGs to the subtitle of DMReport().
  • Houseman() has been parsed from DM.R and the experimental cell composition estimation pipeline has been tidied.
  • tryCatch() is now used for plotDMRs2() to prevent a plotting error from stopping the program .
  • Messaging, error checks, and documentation have been updated.
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