plotDEGPCA: Plot differentially expressed gene principal component...

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Plot differentially expressed gene principal component analysis

Description

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.

Usage

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,
  ...
)

Arguments

object	Object.
i	Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL. For more information: help(topic = "Extract", package = "base")
contrastSamples	logical(1). Only include the samples used to define the contrast passed to DESeq2::results(). This setting will break for complex DESeq2 contrasts (e.g. interaction effect).
alphaThreshold	numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.
baseMeanThreshold	numeric(1) or NULL. Base mean (i.e. average expression across all samples) threshold. If left NULL, will use the cutoff defined in the object. Applies in general to DESeq2 RNA-seq differential expression output.
lfcThreshold	numeric(1) or NULL. Log (base 2) fold change ratio cutoff threshold. If left NULL, will use the cutoff defined in the object.
...	Additional arguments.
DESeqTransform	DESeqTransform.
direction	character(1). Include "both", "up", or "down" directions.

Details

To adjust the annotation columns, modify the colData() of the counts argument, which must contain/extend a SummarizedExperiment.

Value

Plot.

Functions

• plotDEGPCA,DESeqAnalysis-method: Passes to DESeqResults method.

Note

Updated 2021-08-02.

Examples

data(deseq)

## DESeqAnalysis ====
plotDEGPCA(deseq, i = 1L)

steinbaugh/DESeqAnalysis documentation built on June 25, 2022, 7:29 a.m.