PCAPlot: PCA of samples (for DESeq2 object)

In biomics-pasteur-fr/RNADiff: R Tools for RNA-Seq Projects at Institut Pasteur (Biomics Platform)

Description

PCA of samples (for DESeq2 object)

Usage

PCAPlot(dds, group, n = min(500, nrow(counts(dds))),
  type.trans = c("VST", "rlog"), out = TRUE, col = c("lightblue",
  "orange", "MediumVioletRed", "SpringGreen"), axesList = list(c(1, 2),
  c(1, 3)), versionName = ".")

Arguments

dds	a DESeqDataSet object
group	vector of the condition from which each sample belongs
n	number of features to keep among the most variant
type.trans	type of transformation to use ("VST" or "rlog")
out	TRUE to export the figure
col	colors of the bars
axesList	list of couples of axes on which projecting the samples
versionName	versionName of the project

Value

A plot of the two first principal components and the coordinates of the samples

Author(s)

Marie-Agnes Dillies and Hugo Varet

biomics-pasteur-fr/RNADiff documentation built on Aug. 27, 2020, 12:44 a.m.