Plot gene counts as box plots

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.