R/loadGeneLists.R

In goSTAG: A tool to use GO Subtrees to Tag and Annotate Genes within a set

loadGeneLists = function( location, type = "GMT", sep = "\t", header = FALSE, col = 1 ) {
    if( toupper(type) == "GMT" ) {
        ## Load in the gene lists from the GMT file
        raw_data = strsplit( scan( location, what = "character", sep = "\n", quiet = TRUE ), sep )
        gene_lists = lapply( raw_data, function(x) { keep = x!=""; keep[1:2] = FALSE; unique(x[keep]) } )
        names( gene_lists ) = vapply( raw_data, function(x) x[1], character(1) )
        gene_lists
    } else if( toupper(type) == "DIR" ) {
        ## Identify the gene list files within the directory
        gene_list_files = list.files( location )
        gene_list_files_full = paste( sep="", location, "/", gene_list_files )

        ## Load in the gene lists from the files in the directory
        gene_lists = lapply( seq_len( length(gene_list_files) ), function(i) {
            raw_data = read.table( gene_list_files_full[i], header = FALSE, sep = sep )
            if( header == TRUE ) {
                as.character( raw_data[-1,col] )
            } else {
                as.character( raw_data[,col] )
            }
        } )
        names( gene_lists ) = vapply( gene_list_files, function(x) if( substr(x,nchar(x)-3,nchar(x)) == ".txt" ) { substr(x,1,nchar(x)-4) } else { x }, character(1) )
        gene_lists
    } else {
        stop( "Invalid type" )
    }
}