R/leave-k-out-combn.r

In snowball-project/DESnowball: Bagging with Distance-based Regression for Differential Gene Expression Analyses

fs.leave.k.out.combn <-
function(r.idx,dt,classlabel,
           k=2,
           method.agreement=c("euclidean","manhattan","Rand","cRand","NMI",
             "KP","angle","diag","Jaccard","FM","gdbr", "gdbrcpp"),
           method.dist=c("pearson","kendall","spearman","standardizedEuclid",
             "euclidean","euclidean","pearson.u","kendall.u","spearman.u"),
           leave.by=c("count.class","flat","percent.class"),leave.k=1,
           return.value=c("mean","sd"))
  ## leave k out algorithm with exactly every possible combination for classlabel
  {
#    method.agreement <- match.arg(method.agreement)
	return.value<-"mean"
#    return.value <- match.arg(return.value)
    if(is.null(r.idx)) r.idx <- seq(nrow(dt))
#    leave.by <- match.arg(leave.by)
    if(identical(leave.by,"flat")) {
      nu.idx <- t(combn(seq(classlabel),length(classlabel)-leave.k))
    }
    else if(identical(leave.by,"count.class")) {
      nu.idx <- combn.classlabel.idx(classlabel,leave.k=leave.k,leave.k.mode="count")
    }
    else if(identical(leave.by,"percent.class")) {
      nu.idx <- combn.classlabel.idx(classlabel,leave.k=leave.k,leave.k.mode="percent")
    }
    else stop("Unsupported leave.by value!")
	
	## distance
	subset.dt<-dt[r.idx,]
	if(method.dist %in% c("pearson","kendall","spearman"))
		dist.matrix <- (0.5*(1-cor(subset.dt,method=method.dist,use="complete.obs")))
	else if (method.dist %in% c("pearson.u","kendall.u","spearman.u")){
		.method.dist <- sub(".u","",method.dist)
		dist.matrix <- (1-abs(cor(subset.dt,method=.method.dist,use="complete.obs")))
	}
	else if (method.dist == "standardizedEuclid") stop("Not implemented yet!")
	else dist.matrix <- as.matrix(dist(t(subset.dt),method=method.dist))
	
    agreement.measure <- apply(nu.idx,
                               1,
                               fs.agreement.part,
                               r.idx=r.idx,
                               dt=dist.matrix,
                               classlabel=classlabel,
                               k=k,
                               method.agreement=method.agreement,
                               method.dist=method.dist)
    if(identical(return.value,"mean")) return(mean(agreement.measure))
    else if(identical(return.value,"sd")) return(sd(agreement.measure))
    else stop("Unsupported return values")
  }