R/bin_multitest.R

In LyonsZhang/ProgPermute: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries

bin_multitest<-function(i,k,variable,select,testdata,testlevel,levs,position0,position1,method,psigalpha=0.05)
{
  group<-testdata[[variable]]
  n1<-length(position0)
  n2<-length(position1)
  group[sample(position0,k)]<-levs[2]
  group[sample(position1,k)]<-levs[1]
  group<-factor(group)
  if(method=="kruskal")
  {
    otu.test<-apply(testlevel,2,function(x){
      kt<-kruskal.test(x=x,g=group)
      return(data.frame(pv=kt$p.value,es=kt$statistic/sqrt(n1^2+n2^2)))
    })
    otu.test<-do.call(rbind,otu.test)
  }
  else if(method=="wilcox")
  {
    otu.test<-apply(testlevel,2,function(x){
      wt<-wilcox.test(x~group)
      return(data.frame(pv=wt$p.value,es=wt$statistic/sqrt(n1^2+n2^2)))
    })
    otu.test<-do.call(rbind,otu.test)
  }
  #pvalue[,i]<-sort(otu.mk$pv)[1:10]
  psig<-sum(! otu.test$pv>psigalpha,na.rm=T)
  pvalue<--log10(otu.test$pv[select])
  #effectsize<-otu.test$es-median(otu.test$es)
  effectsize<-otu.test$es
  effectsize<-effectsize[select]
  return(list(psig=psig,pvalue=pvalue,effectsize=effectsize))
}