hipA.pvals=read.delim(file="new_out/modA_hip.matrix.tsv", header=T, row.names=1);
#get rid of the extra column: (a column called "X" gets added to the dataframe (because of a tab at the end of each line in the input file))
hipA.pvals = subset(hipA.pvals, select=-c(X))
save(hipA.pvals, file="results/pval.matrices/A/hipA.pvals.RData")

livA.pvals=read.delim(file="new_out/modA_liv.matrix.tsv", header=T, row.names=1);
livA.pvals = subset(livA.pvals, select=-c(X))
save(livA.pvals, file="results/pval.matrices/A/livA.pvals.RData")

lunA.pvals=read.delim(file="new_out/modA_lun.matrix.tsv", header=T, row.names=1);
lunA.pvals = subset(lunA.pvals, select=-c(X))
save(lunA.pvals, file="results/pval.matrices/A/lunA.pvals.RData")

go2name <- read.delim(file='lib/GO2name.txt', sep='\t')

hip.genes.pvals=read.delim(file="new_out/modA_hip.pval_0.001andBelow.i10000.txt", header=T)
head(hip.genes.pvals)
unique(hip.genes.pvals$module)
unique(hip.genes.pvals$phenotype)

getLowPvals <- function(pvalues, thr){
 values=pvalues[pvalues< thr]
 phenotypes=colnames(pvalues)[col(pvalues)[pvalues< thr]]
 modules=rownames(pvalues)[row(pvalues)[pvalues< thr]]
 d=data.frame(pval=values, phenos=phenotypes, module=modules)
 return(d)
}

hip.lowpvals=getLowPvals(hipA.pvals, 0.001)

#GO ANALYSIS
M=read.table("../go_analysis/modA_hip_mod_genes.mat", header=T);
load("GOM.RData")

hipA.pval.go=matrix(NA, nrow=dim(GOM)[2],ncol=dim(M)[2])
colnames(hipA.pval.go)=colnames(M)
rownames(hipA.pval.go)=colnames(GOM)

fisher.func <- function(X, genes){
	X <- as.factor(X); 
	if (nlevels(X) == 2){
		f<-fisher.test(X,genes);
		return(f$p.value)
	} 
	else return(1)
}
	
for(i in 1: dim(M)[2]){
	col=M[,i]
	hipA.pval.go[,i]=unlist(apply(X=GOM,FUN=fisher.func, MARGIN=2,col))
}

save(hipA.pval.go, "/data/www/go_analysis/hipA.pval.go.RData")

load("../go_analysis/hipA.pval.go.RData")
go2name <- read.delim(file='../go_analysis/GO2name.txt', sep='\t')

getLowPvals <- function(pvalues, go2name, thr){
         values=pvalues[pvalues< thr]
        goterms=rownames(pvalues)[row(pvalues)[pvalues< thr]]
        modules=colnames(pvalues)[col(pvalues)[pvalues< thr]]
        matches=match(goterms, go2name[,1])
        d=data.frame(pval=values, goterm=goterms, module=modules,desc=go2name[matches,2])
        return(d)
}

cutoff=0.001;
hip.lowpvals=getLowPvals(hipA.pval.go, go2name, cutoff)

head(hip.lowpvals)
hip.lowpvals.ordered=hip.lowpvals[order(hip.lowpvals$pval),]

head(hip.lowpvals.ordered)