SARTools (version 1.6.2)

exploreCounts: Explore counts structure

Description

Explore counts structure: PCA (DESeq2) or MDS (edgeR) and clustering

Usage

exploreCounts(object, group, typeTrans = "VST", gene.selection = "pairwise",
  col = c("lightblue", "orange", "MediumVioletRed", "SpringGreen"))

Arguments

object

a DESeqDataSet from DESeq2 or DGEList object from edgeR

group

factor vector of the condition from which each sample belongs

typeTrans

transformation method for PCA/clustering with DESeq2: "VST" or "rlog"

gene.selection

selection of the features in MDSPlot ("pairwise" by default)

col

colors used for the PCA/MDS (one per biological condition)

Value

A list containing the dds object and the results object