plotDEGHeatmap usage clarification

[mjsteinbaugh]

See related bcbioRNASeq issue from @Xiaofei-git: hbc/bcbioRNASeq#181

Also refer to corresponding bcbioRNASeq differential expression template for usage in bcbio RNA-seq analysis workflow: https://github.com/hbc/bcbioRNASeq/blob/master/inst/rmarkdown/templates/02-differential-expression/skeleton/skeleton.Rmd

plotDEGHeatmap is an S4 generic function defined in the AcidGenerics package. Refer to this Bioconductor article for a history of the S4 system in R/Bioconductor.

Recommended approach for heatmap visualization of differentially expressed genes (DEGs) from DESeq2 output via plotDEGHeatmap first requires that the DESeqDataSet, DESeqTransform, and DESeqResults are packaged into a DESeqAnalysis object via the DESeqAnalysis() function.

Refer to the help documentation for usage details.

help(topic = "plotDEGHeatmap", package = "DESeqAnalysis")

Alternatively, here's how to look up supported methods for the desired generic function:

methods("plotDEGHeatmap")
## [1] plotDEGHeatmap,DESeqAnalysis-method plotDEGHeatmap,DESeqResults-method
## see '?methods' for accessing help and source code

showMethods("plotDEGHeatmap")
## Function: plotDEGHeatmap (package AcidGenerics)
## object="DESeqAnalysis"
## object="DESeqResults"