R/massMap.R

In JiyuanHu/massMap: massMap: a two-stage microbial association mapping framework with advanced FDR control

massMap <-
function(X=NULL,Y=NULL,obstime = NULL,delta= NULL,otu.tab,is.count.otu.tab = TRUE,tax.tab,tree=NULL,outcome.trait=outcome.traits,
	screening.rank= 'Family',target.rank= ranks,alpha=0.05,n.perm=1e4){
	set.seed(1234)
  outcome.trait = match.arg(outcome.trait,outcome.traits)
  screening.rank= match.arg(screening.rank,ranks)
  target.rank= match.arg(target.rank,ranks)
  if(outcome.trait =='survival'){
    if(is.null(tree) | is.count.otu.tab==FALSE){
      print('Unfortunately massMap is not applicable to perform the microbial survival association analysis for relative abundance data or microbiome data with no phylogenetic tree')
    }else{
	    d = massMap.Surv(X,obstime,delta,otu.tab,is.count.otu.tab,tax.tab,tree,
	screening.rank,target.rank,alpha=alpha,n.perm)
    }
  }else{
	d = massMap.glm (X,Y,otu.tab,is.count.otu.tab,tax.tab,tree,outcome.trait,
	screening.rank,target.rank,alpha=alpha,n.perm)
  }
  return(d)
}