R/convertSifToGmt.R

In paxtoolsr: PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

#' Convert SIF to GMT 
#' 
#' @param sif a data.frame representing a SIF (Simple Interaction Format)
#' @param name the name of the gene set
#' @param returnSmallMolecules a boolean whether to return genes 
#'   or small molecules in the gene set
#' 
#' @return a list with one entry being a vector 
#' 
#' @examples 
#' sif <- readSif(system.file("extdata", "test_sif.txt", package="paxtoolsr"))
#' gmt <- convertSifToGmt(sif)
#' 
#' @concept paxtoolsr
#' @export
convertSifToGmt <- function(sif, name="gmt", returnSmallMolecules=FALSE) {
    ids <- unique(c(sif$PARTICIPANT_A, sif$PARTICIPANT_B))
    
    if(returnSmallMolecules) {
        idx <- grepl("^CHEBI", ids)
    } else {
        idx <- !grepl("^CHEBI", ids)
    }
    
    results <- list()
    results[[name]] <- sort(ids[idx])
    
    return(results)
}