gmtGene2Cat: gmtGene2Cat

In PathwaySplice: An R Package for Unbiased Splicing Pathway Analysis

Description

Obtains all pathways associated with a set of genes

Usage

gmtGene2Cat(pathway.file, gene.anno.file = NULL, genomeID = c("mm10",
  "hg19", "hg38"))

Arguments

pathway.file	Input file for the gene sets in GMT format, must be in gene symbols
gene.anno.file	Gene annotation file that facilitate gene id conversions when gene ids in RNA-Seq data and pathway.file differ. If not specified, gmtGene2cat relies on gene annotations provided by R package AnnotationHub.
genomeID	Genome to be used. Options are 'mm10','hg19' or 'hg38'.

Details

This function reads a gene set file in https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29, and returns a list with its name being a gene id, and each element of the list being the pathways associated with the gene. When gene ids in RNA-Seq data differ from those in pathway database, gene.anno.file facilitate gene id conversions. Users can prepare this file based on the format of the example gene annotation file at https://raw.githubusercontent.com/aiminy/GOSJ/master/data/gene_annotation.txt

Value

A list where each entry is named by a gene and contains a vector of all the pathways associated with the gene

Examples

#using local file for pathways database
dir.name <- system.file('extdata', package='PathwaySplice')
hallmark.local.pathways <- file.path(dir.name,'h.all.v6.0.symbols.gmt.txt')
hlp <- gmtGene2Cat(hallmark.local.pathways, genomeID='hg19')

## Not run: 
#using url for pathways database linked to a website
hallmark.url.pathways <- paste0('https://raw.githubusercontent.com/SCCC-BBC',
                   '/PathwaySplice/development/inst/extdata',
                     '/h.all.v6.0.symbols.gmt.txt')
hup <- gmtGene2Cat(hallmark.url.pathways, genomeID='hg19')
## End(Not run)

PathwaySplice documentation built on April 28, 2020, 7:44 p.m.