R/write.regulon.R

In federicogiorgi/aracne.networks: ARACNe-inferred gene networks from TCGA tumor datasets

write.regulon<-function(
    regulon,
    file="",
    sep="\t",
    header=TRUE,
    n=Inf,
    regulator=NULL
){
    if(header){
        cat(paste0("Regulator\tTarget\tMoA\tlikelihood\n"),file=file)
    }
    nn<-0
    if(is.null(regulator)){
        for(tf in names(regulon)){
            x<-regulon[[tf]]
            targets<-names(x$tfmode)
            moas<-x$tfmode
            likelihoods<-x$likelihood
            tab<-cbind(rep(tf,length(targets)),targets,moas,likelihoods)
            i<-1
            while(nn<n&i<=nrow(tab)){
                cat(
                    tab[i,],
                    file=file,
                    append=TRUE,
                    sep=sep
                )
                cat("\n",file=file,append=TRUE)
                nn<-nn+1
                i<-i+1
            }
        }
    } else {
        tf<-regulator
        x<-regulon[[tf]]
        targets<-names(x$tfmode)
        moas<-x$tfmode
        likelihoods<-x$likelihood
        tab<-cbind(rep(tf,length(targets)),targets,moas,likelihoods)
        i<-1
        while(nn<n&i<=nrow(tab)){
            cat(
                tab[i,],
                file=file,
                append=TRUE,
                sep=sep
            )
            cat("\n",file=file,append=TRUE)
            nn<-nn+1
            i<-i+1
        }
    }

}