goSemSim.R

#!/usr/bin/env Rscript
#suppressMessages(library(GOSim))
suppressMessages(library(GOSemSim))
suppressMessages(library(getopt))

spec = matrix(c(
  'outdir', 'o', 1, 'character',
  'help', 'h', 0, 'logical'
), byrow=TRUE, ncol=4)

opt <- getopt(spec)

if (is.null(opt$outdir) || !is.null(opt$help)) {
  cat(getopt(spec, usage=TRUE))
  q(status=1)
}
loc1 = opt$outdir

hsGO = godata('org.Hs.eg.db',ont='BP')

l1 = list()
l1$SelfSufficiencyInGrowthSignals = c('GO:0009967','GO:0030307','GO:0008284','GO:0045787','GO:0007165')
l1$InsensitivityToAntigrowthSignals = c('GO:0009968','GO:0030308','GO:0008285','GO:0045786','GO:0007165')
l1$EvadingApoptosis = c('GO:0043069','GO:0043066')
l1$LimitlessReplicativePotential = c('GO:0001302','GO:0032206','GO:0090398')
l1$SustainedAngiogenesis = c('GO:0045765','GO:0045766','GO:0030949','GO:0001570')
l1$TissueInvasionAndMetastasis = c('GO:0042060','GO:0007162','GO:0033631','GO:0044331','GO:0001837','GO:0016477','GO:0048870','GO:0007155')
l1$GenomeInstabilityAndMutation = c('GO:0051276','GO:0045005','GO:0006281')
l1$TumorPromotingInflammation = c('GO:0002419','GO:0002420','GO:0002857','GO:0002842','GO:0002367','GO:0050776')
l1$ReprogrammingEnergyMetabolism = c('GO:0006096','GO:0071456')
l1$EvadingImmuneDetection = c('GO:0002837','GO:0002418','GO:0002367','GO:0050776')


d1 = read.csv(paste(loc1, 'biclusterEnrichment_GOBP.csv', sep='/'),header=T,row.names=1)
l2 = list()
for(cluster in rownames(d1)) {
    l2[[cluster]] = intersect(strsplit(as.character(d1[cluster,2]),';')[[1]],hsGO@geneAnno$GO)
}

hallmarks = matrix(ncol=length(names(l1)), nrow=length(names(l2)), dimnames=list(names(l2), names(l1)))
for(cluster in names(l2)) {
    if (!(length(l2[[cluster]])==0)) {
        for(hallmark in names(l1)) {
            print(cluster)
            #d2 = getTermSim(c(l2[[cluster]],l1[[hallmark]]),method='JiangConrath')
            #hallmarks[cluster,hallmark] = max(d2[1:length(l2[[cluster]]),-(1:length(l2[[cluster]]))],na.rm=T)
            hallmarks[cluster,hallmark] = mgoSim(l2[[cluster]], l1[[hallmark]], semData=hsGO, measure='Jiang', combine='max')
        }
    }
}

write.csv(hallmarks,paste(loc1, 'jiangConrath_hallmarks.csv', sep='/'))