createLimmaOutput: using limma package to do differential expression analysis

In xianxiongma/mxxfpkg:

Description

using limma package to do differential expression analysis

Usage

createLimmaOutput(
  GSE = "GSE65858",
  columnGSE = 1:ncol(eset),
  GPL = "GPL10558",
  method = "max",
  columnGPL = NULL,
  group = NULL,
  sepTitle = "_",
  groupIndex = 5,
  logFC = 1.5,
  pvalue = 0.05
)

Arguments

GSE	a GSE id or a data.frame. if a data.frame, first column must be gene symbol.
columnGSE	which column should be used to do differential expression analysis.
GPL	the matched GPL platform of GSE id.
method	max or mean.
columnGPL	which column to convert probe id.
group	if GSE is a data.frame, a group vector should be provided. Otherwise omit.
sepTitle	separator of the title.
groupIndex	which vector should be taken after the title was split.
logFC	log fold change.
pvalue	cutoff to screen result.

Value

generate a differential expression analysis results.

Examples

createLimmaOutput(GSE = fpkm, group = group)
createLimmaOutput(GSE="GSE19136",columnGSE = c(1,2,4,5,7,8,10,11),GPL='GPL570', method="max", columnGPL=c(1,11),logFC=1.5,pvalue=0.05)

xianxiongma/mxxfpkg documentation built on May 12, 2021, 6:56 a.m.