Write a pathwayCollection Object to a .gmt File

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

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''.

Value

NULL. Output written to the file path specified.

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

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
#> Object with Class(es) 'pathwayCollection', 'list' [package 'pathwayPCA'] with 3 elements: 
#>  $ pathways   :List of 3
#>  $ TERMS      : chr [1:3] "C-or-f_paths" ...
#>  $ description: chr [1:3] "these are" ...

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