DMRichR v1.6.1
New Features:
DMRichR::slimGO()
utilizes rrvgo and replacesDMRichR::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()
andDMRichR::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()
, andDMRichR::CGi()
) and plot (DMRichR::PCA()
andDMRichR::densityPlot()
) DMRichR::processBismark()
will now automatically convert ranges to UCSC style, drop sex chromosomes ifsexCheck == TRUE
and both sexes are detected, and assign colors for DMR and block plotsDMRichR::imprintOverlap()
fix for non-humansDMRichR::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