OneLinerOmics: One-liner RNA-seq and ChIP-seq Analyses

Description Usage Arguments Details Author(s) References See Also

PlotEnrichments performs and plots enrichment analyses for a list of DESeqResults objects as generated by RunDESeq2 or ProcessDEGs or a list of data.frames as generated by RunDiffBind or ProcessDBRs. It queries the enrichr web server to do so. Results are saved both as tables and plots.

PlotEnrichments(
  res.list,
  outpath,
  padj.thresh,
  fc.thresh,
  libraries,
  chip = FALSE
)

`res.list`	Either: A named list containing DESeqResults objects for all comparisons generated by `ProcessDEGs`, or A named list containing two or three csAnno objects for a given comparison generated by `ProcessDBRs` if `chip = TRUE`. First must contain all DBRs, second/third contain DBRs up in one group versus the other.
`outpath`	Path to directory to be used for output. Additional directories will be generated within this folder.
`padj.thresh`	Number indicating the adjusted p-value cutoff to be used for determining "significant" differential expression or differential binding (if `chip = TRUE`).
`fc.thresh`	Number indicating the log2 fold-change cutoff to be used for determining "significant" differential expression. or differential binding (if `chip = TRUE`).
`libraries`	A vector of valid `enrichR` libraries to test the genes against.
`chip`	Boolean indicating whether `res.list` is the results from `dba.analyze`.

Available libraries can be viewed with listEnrichrDbs from the enrichR package.

The enrichr web server can be found at https://amp.pharm.mssm.edu/Enrichr/. If you use this function, you should be sure to cite the original authors.

Jared Andrews

Kuleshov MV, Jones MR, Rouillard AD, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377

RunEnrichr, VizEnrichments, and enrichr for additional enrichment options.

ProcessDEGs for generating DESeqResults objects. ProcessDBRs, for generating csAnno objects.

j-andrews7/OneLinerOmics documentation built on Sept. 9, 2021, 11 a.m.