exploreCounts: Explore counts structure

In PF2-pasteur-fr/SARTools: Statistical Analysis of RNA-Seq Tools

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"),
  ggplot_theme = theme_light()
)

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)
ggplot_theme	ggplot2 theme function (theme_light() by default)

Value

A list containing the dds object and the results object

Author(s)

Hugo Varet

PF2-pasteur-fr/SARTools documentation built on April 6, 2022, 2:24 a.m.