convertGMT: Convert gmt formatted pathway file to the Pathway ID, Entrez,...

In guldenolgun/NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Convert gmt formatted pathway file to the Pathway ID, Entrez, symbol formatted data frame

Description

Convert gmt formatted pathway file to the Pathway ID, Entrez, symbol formatted data frame

Usage

convertGMT(gmtName, org_assembly, isSymbol = FALSE)

Arguments

gmtName	Custom pathway gmt file
org_assembly	Genome assembly of interest for the analysis. Possible assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat, "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and "hg38" for human
isSymbol	Boolean variable that hold the gene format of the gmt file. If it is set as TRUE, gene format of the gmt file should be symbol. Otherwise, gene format should be ENTREZ ID. By default, it is FALSE.

Value

return data frame

guldenolgun/NoRCE documentation built on Oct. 21, 2022, 11:48 a.m.