edgeR-methods: Extension for the edgeR package

In easyRNASeq: Count summarization and normalization for RNA-Seq data

Description

This method extends the edgeR package by offering the functionality to plot the effect of the normalization factor.

Usage

## S4 method for signature 'DGEList,character,character'
plotNormalizationFactors(
  obj = DGEList(),
  cond1 = character(1),
  cond2 = character(1)
)

Arguments

obj	An object of class DGEList
cond1	A character string describing the first condition
cond2	A character string describing the second condition

Value

none

Author(s)

Nicolas Delhomme

Examples

	## Not run: 
	## create the object
	dgeList <- DGEList(counts,group)
	## calculate the sie factors
	dgeList <- calcNormFactors(dgeList)
	## plot them
	apply(combn(rownames(dgeList$samples),2),
		2,
		function(co,obj){plotNormalizationFactors(obj,co[1],co[2])},dgeList)
	
## End(Not run)

easyRNASeq documentation built on April 30, 2020, 2 a.m.