write_gmt: Write a 'pathwayCollection' Object to a '.gmt' File

In pathwayPCA: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

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")

pathwayPCA documentation built on Dec. 15, 2020, 6:14 p.m.