R/FromEbfit2Table_GSVA.R

In mssm-msf-2019/BiostatsALL:

#' creates an output table including all pathways in ebfit. Like FromEbfit2Table, but does not include FCH columns as they dont make sense in the GSVA context.
#' @description For each contratst in ebfit, a matrix with lgFCH, FCH,pvalue , fdr and Status (1 up,-1 doen,0 non sign) is created using pre-specified cut-oofs
#' @param ebfit output of eBayes
#' @param adj adjustment method for multiple hypothesis
#' @param mcut cutoff for FCH (to be used for Status columns)
#' @param pcut cutoff for pvalue/FDR  (to be used for Status columns)
#' @param annot should the dat be annotated? If TRUE it will check if tehre is annotTab or otherwise whatever annotation is stored in ebfit$genes
#' @param annotTab annotation database
#' @param first.ann.cols Indicates which elements of the annotation db, should appear before all the comparisons.
#' @examples
#' Tab<-FromEbfit2Table_GSVA(ebfit,pcut=0.05,mcut=2)

FromEbfit2Table_GSVA<-function(ebfit,adj='BH',mcut=2,pcut=0.05, annot=FALSE, annotTab=NULL, first.ann.cols=c('SYMBOL','GENENAME')){

  ctrnames<-gsub("_",".",colnames(ebfit$coef),fixed=TRUE)

  logFCHs<-round(ebfit$coef,2); colnames(logFCHs)<-paste('lgFCH',ctrnames,sep='_')

  reformatps<-function(p){as.numeric(format(p,digit=3,drop0trailing = TRUE))}
  pvals<-ebfit$p.value; colnames(pvals)<-paste('pvals',ctrnames,sep='_')
  fdrs<-apply(pvals,2,p.adjust,adj); colnames(fdrs)<-paste('fdrs',ctrnames,sep='_')
  pvals<-apply(pvals,2, reformatps)
  fdrs<-apply(fdrs,2, reformatps)

  D<-decideTests(ebfit,method="separate",adjust.method=adj,p.value=pcut,lfc=log2(mcut))
  colnames(D)<-paste('StatusFCH',mcut,ifelse(adj=='none','P','FDR'),pcut,"_",ctrnames,sep='')
  Tab<-cbind(logFCHs,pvals,fdrs,D); cn<-colnames(Tab)

  CNS<-sapply(colnames(Tab),function(x){gsub(paste(strsplit(x,'_')[[1]][1],"_",sep=''),"",x)})
  Tab<-(Tab[,sapply(ctrnames,function(cn,CNS){which(CNS==cn)},CNS)])

  return(Tab)
}