Nothing
############################################################
#' read functional gene sets
#' @param inputFile Input file name
#' @param geneName Gene name lists
#' @param minSupport Minimum support
#' @return Functional gene set
#' @export
############################################################
# DECODE (c) Copyright 2014 by The Hong Kong Polytechnic University, Department of Health Technology and Informatics
# Written by Thomas Lui
# Permission is granted to copy and use this program provided no fee is
# charged for it and provided that this copyright notice is not removed.
##########################################################################
getPathway = function(inputFile,geneName,minSupport) {
inFile = file(inputFile, open = "r")
pathwayName="";
pathwayCategory="";
pathwayIndexSet=list();
pathwayCount=0;
size_pathwayIndexSet=0;
pathway=data.frame(name=character(), categoryInfo=character(),indexSet=list(), size_indexSet=double(),stringsAsFactors = FALSE)
while (TRUE) {
# read a line
oneLine = readLines(inFile, n = 1, warn = FALSE)
if (length(oneLine)== 0) {
break
}
if (pathwayCount %% 100 ==0) {
# print(pathwayCount)
}
oneLineArray = unlist(strsplit(oneLine, "\t"))
onePathwayName = oneLineArray[1]
onePathwayCategory= oneLineArray[2]
size_oneLineArray = length(oneLineArray)
tempPathwayIndexSetSize=0
onePathwayGeneSet=oneLineArray[3:size_oneLineArray]
onePathwayGeneSetIndex = match(onePathwayGeneSet,geneName, nomatch=-1)
onePathwayGeneSetIndex =onePathwayGeneSetIndex[onePathwayGeneSetIndex != -1]
size_onePathwayGeneSetIndex = length(onePathwayGeneSetIndex)
#at least there are some matches (>=minSupport) of this pathway set to the genes of the gene expression data
if (size_onePathwayGeneSetIndex >=minSupport) {
pathwayCount=pathwayCount+1
pathway[pathwayCount,"name"]= onePathwayName
pathway[pathwayCount,"categoryInfo"]=onePathwayCategory
pathway$indexSet[[pathwayCount]] =onePathwayGeneSetIndex # assign list of numbers
pathway[pathwayCount,"size_indexSet"]=size_onePathwayGeneSetIndex
}
}
close(inFile)
return(pathway)
}
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