write_gmt {pathwayPCA} | R Documentation

## Write a `pathwayCollection` Object to a `.gmt` File

### Description

Write a `pathwayCollection` object as a pathways list file in Gene Matrix Transposed (`.gmt`) format.

### Usage

    write_gmt(pathwayCollection, file, setType = c("pathways", "genes", "regions"))

### Arguments

`pathwayCollection` | A `pathwayCollection` list of sets. This list contains the following two or three elements: 'setType' : A named list of character vectors. Each vector contains the names of the individual genes, sites, or CpGs within that set as a vector of character strings. If you are using genes, these genes can be represented by HGNC gene symbols, Entrez IDs, Ensembl IDs, GO terms, etc. `TERMS` : A character vector the same length as the 'setType' list with the proper names of the sets. `description` : An optional character vector the same length as the 'setType' list with a note on that set (such as a url to the description if the set is a pathway). If this element of the `pathwayCollection` is `NULL`, then the file will be written with `""` (the empty character string) as its second field in each line.
`file` | Either a character string naming a file or a connection open for writing. File names should end in `.gmt` for clarity.
`setType` | What is the type of the set: pathway set of gene, gene sites in RNA or DNA, or regions of CpGs. Defaults to `''pathway''`.

### Details

See the Broad Institute's "Data Formats" page for a description of the Gene Matrix Transposed file format: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29

### Value

NULL. Output written to the file path specified.

### See Also

`print.pathwayCollection`; `read_gmt`

### Examples

      # Toy pathway set
      toy_pathwayCollection <- list(
        pathways = list(
          c("C1orf27", "NR5A1", "BLOC1S4", "C4orf50"),
          c("TARS2", "DUSP5", "GPR88"),
          c("TRX-CAT3-1", "LINC01333", "LINC01499", "LINC01046", "LINC01149")
        ),
        TERMS = c("C-or-f_paths", "randomPath2", "randomLINCs"),
        description = c("these are", "totally made up", "pathways")
      )
      class(toy_pathwayCollection) <- c("pathwayCollection", "list")
      toy_pathwayCollection

      # write_gmt(toy_pathwayCollection, file = "example_pathway.gmt")

[Package pathwayPCA version 1.10.0 Index]