plotDEGPCA: Plot differentially expressed gene principal component...

Description Usage Arguments Details Value Functions Note Examples

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

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plotDEGPCA(object, ...)

## S4 method for signature 'DESeqResults'
plotDEGPCA(
  object,
  DESeqTransform,
  alphaThreshold = NULL,
  lfcThreshold = NULL,
  baseMeanThreshold = NULL,
  direction = c("both", "up", "down"),
  ...
)

## S4 method for signature 'DESeqAnalysis'
plotDEGPCA(object, i, contrastSamples = FALSE, ...)

Arguments

object

Object.

DESeqTransform

DESeqTransform.

alphaThreshold

numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.

lfcThreshold

numeric(1) or NULL. Log (base 2) fold change ratio cutoff threshold. 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.

direction

character(1). Include "both", "up", or "down" directions.

...

Additional arguments.

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). Experimental. 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).

Details

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

Value

Plot.

Functions

Note

Updated 2020-08-25.

Examples

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data(deseq)

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

steinbaugh/DESeqAnalysis documentation built on Oct. 15, 2020, 2:02 a.m.