readGmt {BioQC} | R Documentation

## Read in gene-sets from a GMT file

### Description

Read in gene-sets from a GMT file

### Usage

    readGmt(..., uniqGenes = TRUE, namespace = NULL)

### Arguments

`...` | Named or unnamed characater string vector, giving file names of one or more GMT format files.
`uniqGenes` | Logical, whether duplicated genes should be removed
`namespace` | Character, namespace of the gene-set. It can be used to specify namespace or sources of the gene-sets. If `NULL` is given, so no namespace is used and all gene-sets are assumed to come from the same unspecified namespace. The option can be helpful when gene-sets from multiple namespaces are jointly used.

### Value

A `GmtList` object, which is a S4-class wrapper of a list. Each element in the object is a list of (at least) three items:

- gene-set name (field `name`), character string, accessible with `gsName`

- gene-set description (field `desc`), character string, accessible with `gsDesc`

- genes (field `genes`), a vector of character strings, , accessible with `gsGenes`

- namespace (field `namespace`), accessible with `gsNamespace`

### Note

Currently, when `namespace` is set as `NULL`, no namespace is used. This may change in the future, since we may use file base name as the default namespace.

### Examples

    gmt_file <- system.file("extdata/exp.tissuemark.affy.roche.symbols.gmt", package="BioQC")
    gmt_list <- readGmt(gmt_file)
    gmt_nonUniqGenes_list <- readGmt(gmt_file, uniqGenes=FALSE)
    gmt_namespace_list <- readGmt(gmt_file, uniqGenes=FALSE, namespace="myNamespace")

    ## suppose we have two lists of gene-sets to read in
    test_gmt_file <- system.file("extdata/test.gmt", package="BioQC")
    gmt_twons_list <- readGmt(gmt_file, test_gmt_file, namespace=c("BioQC", "test"))
    ## alternatively
    gmt_twons_list <- readGmt(BioQC=gmt_file, test=test_gmt_file)

[Package BioQC version 1.22.0 Index]