plotDEGPCA | R Documentation |
This function is an extension of plotPCA()
that is optimized for automatic
handling of differentially expressed genes, rather than requiring manual
input of a gene vector or subset object.
plotDEGPCA(object, ...) ## S4 method for signature 'DESeqAnalysis' plotDEGPCA( object, i, contrastSamples = FALSE, alphaThreshold = NULL, baseMeanThreshold = NULL, lfcThreshold = NULL, ... ) ## S4 method for signature 'DESeqResults' plotDEGPCA( object, DESeqTransform, direction = c("both", "up", "down"), alphaThreshold = NULL, baseMeanThreshold = NULL, lfcThreshold = NULL, ... )
object |
Object. |
i |
Indices specifying elements to extract or replace. Indices are For more information: help(topic = "Extract", package = "base") |
contrastSamples |
|
alphaThreshold |
|
baseMeanThreshold |
|
lfcThreshold |
|
... |
Additional arguments. |
DESeqTransform |
|
direction |
|
To adjust the annotation columns, modify the colData()
of the counts
argument, which must contain/extend a SummarizedExperiment
.
Plot.
plotDEGPCA,DESeqAnalysis-method
: Passes to DESeqResults
method.
Updated 2021-08-02.
data(deseq) ## DESeqAnalysis ==== plotDEGPCA(deseq, i = 1L)
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