SARTools (version 1.6.2)

MDSPlot: MDS plot (for edgeR objects)

Description

Multi-Dimensional Scaling plot of samples based on the 500 most variant features (for edgeR analyses)

Usage

MDSPlot(dge, group, n = min(500, nrow(dge$counts)),
  gene.selection = c("pairwise", "common"), col = c("lightblue", "orange",
  "MediumVioletRed", "SpringGreen"), outfile = TRUE)

Arguments

dge

a DGEList object

group

vector of the condition from which each sample belongs

n

number of features to keep among the most variant

gene.selection

"pairwise" to choose the top features separately for each pairwise comparison between the samples or "common" to select the same features for all comparisons. Only used when method="logFC"

col

colors to use (one per biological condition)

outfile

TRUE to export the figure in a png file

Value

A file named MDS.png in the figures directory