gmtGene2Cat {PathwaySplice} | R Documentation

## gmtGene2Cat

### 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)

[Package PathwaySplice version 1.4.0 Index]