FromEbfit2DEGTable: creates an output table including genes that are declared...

In mssm-msf-2019/BiostatsALL:

Description

For each contratst in ebfit, a matrix with lgFCH, FCH,pvalue , fdr and Status (1 up,-1 doen,0 non sign) is created using pre-specified cut-oofs

Usage

FromEbfit2DEGTable(ebfit, adj = "BH", mcut = 2, pcut = 0.05,
  annot = TRUE, annotTab = NULL)

Arguments

ebfit	output of eBayes
adj	adjustment method for multiple hypothesis
mcut	cutoff for FCH (to be used for Status columns)
pcut	cutoff for pvalue/FDR (to be used for Status columns)
annot	should the dat be annotated? If TRUE it will check if tehre is annotTab or otherwise whatever annotation is stored in ebfit$genes
annotTab	annotation database

Examples

TabDEG<-FromEbfit2DEGTable(ebfit,pcut=0.05,mcut=2)

mssm-msf-2019/BiostatsALL documentation built on May 22, 2019, 12:16 p.m.