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DMRichR v1.6.1

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@ben-laufer ben-laufer released this 12 Apr 16:47
· 24 commits to master since this release
82ee1f2

New Features:

  • DMRichR::slimGO() utilizes rrvgo and replaces DMRichR::REVIGO() due to REVIGO website update
  • Support for ensembldb (--ensembl argument for DM.R), which improves annotations for non-model organisms
  • DMRichR::getCpGs() is a new CpG island/feature annotation system that supports almost all organisms
  • Plotting of exons and CpG feature tracks in the DMR and block plots for almost all organisms via DMRichR::getCpGs() and DMRichR::getExons()
  • Interactive Global, 20Kb Window, and CpG Island MDS plots from Glimma

Improvements:

  • The globalPlots approach has been redone to create separate functions to extract (DMRichR::windows(), DMRichR::CpGs(), and DMRichR::CGi()) and plot (DMRichR::PCA() and DMRichR::densityPlot())
  • DMRichR::processBismark() will now automatically convert ranges to UCSC style, drop sex chromosomes if sexCheck == TRUE and both sexes are detected, and assign colors for DMR and block plots
  • DMRichR::imprintOverlap() fix for non-humans
  • DMRichR::GOfuncR() now supports analyses outside of DM.R that do not have exact overlap between the DMRs and background regions
  • An argument to not run GOfuncR (--GOfuncR) has been added to DM.R
  • enrichR now selects organism specific sites/databases if available
  • rGREAT has been changed to "oneClosest" rule
  • Gene ontologies will only run for all DMRs, the additional stratification of hypermethylated and hypomethylated has been removed
  • DMRichR::GOplot() now has increased font size and text truncation for long terms