PlotRNABoxplots: Plot gene counts as box plots

In j-andrews7/AndrewsBCellLymphoma: One-liner RNA-seq and ChIP-seq Analyses

Description

Plot gene counts as box plots

Usage

PlotRNABoxplots(
  res.list,
  dds,
  rld,
  outpath,
  padj.thresh,
  fc.thresh,
  top.n,
  level
)

Arguments

res.list	Named List containing DESeqResults objects for all comparisons generated by ProcessDEGs.
dds	A DESeqDataSet object as returned by DESeq or RunDESeq2.
rld	A RangedSummarizedExperiment object of rlog transformed counts as returned by RunDESeq2.
outpath	Path to directory to be used for output.
padj.thresh	Number indicating the adjusted p-value cutoff to be used for determining "significant" differential expression.
fc.thresh	Number indicating the log2 fold-change cutoff to be used for determining "significant" differential expression.
top.n	Number of differentially expressed genes to create boxplots for, ranked by adj. p-value after applying padj.thresh and fc.thresh thresholds.
level	String defining variable of interest.

Author(s)

Jared Andrews

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