runEdgeRNorm: Function runEdgeRNorm (edgeR normlization )

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Returns a DGEobj containing DGEList object representing the result of edgeR TMM normalization.

Usage

runEdgeRNorm(
  dgeObj,
  normMethod = "TMM",
  plotFile = "TMM_Norm.Factors.PNG",
  plotLabels = NULL
)

Arguments

dgeObj	A DGEobj data structure containing counts, design data and gene annotation
normMethod	One of "TMM", "RLE", "upperquartile" or "none". Default = "TMM"
plotFile	Enable a Barplot of the norm.factors produced (Default = "Norm.Factors.PNG") Set to NULL to disable the plot.
plotLabels	Sample labels for the plot. Length must equal the number of samples. (Default = NULL; sample number will be displayed)

Value

A DGEObj with a normalized DGEList added.

Author(s)

John Thompson, [e-mail]

Examples

MyDgeObj <- runEdgeRNorm (RSE)

MyDgeObj <- runEdgeRNorm (MyDgeObj)

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.