Nothing
CCPROMISE<-function(geneSet,
ESet,
MSet,
promise.pattern,
strat.var=NULL,
prlbl=NULL,
EMlbl=c('Expr', 'Mthyl'),
nbperm=FALSE,
max.ntail=100,
nperms=10000,
seed=13)
{
Edat<-exprs(ESet)
Mdat<-exprs(MSet)
pheDat<-phenoData(ESet)
phdat<-pData(pheDat)
Edat<-Edat[, is.element(dimnames(Edat)[[2]], dimnames(Mdat)[[2]]) &
is.element(dimnames(Edat)[[2]], dimnames(phdat)[[1]])]
Mdat<-Mdat[, is.element(dimnames(Mdat)[[2]], dimnames(Edat)[[2]]) &
is.element(dimnames(Mdat)[[2]], dimnames(phdat)[[1]])]
phdat<-phdat[is.element(dimnames(phdat)[[1]], dimnames(Edat)[[2]])&
is.element(dimnames(phdat)[[1]], dimnames(Mdat)[[2]]), ]
#data checking
if(any(dimnames(Edat)[[2]]!=dimnames(Mdat)[[2]]))
{
message('Data Error!!!!!!!!!!!!!!!!!!!!!!!!!')
break()
}
if(any(dimnames(Edat)[[2]]!=dimnames(phdat)[[1]] ))
{
message('Data Error!!!!!!!!!!!!!!!!!!!!!!!!!')
break()
}
canres<-CANN(geneSet=geneSet, Edat=Edat, Mdat=Mdat, EMlbl=EMlbl, phdat=phdat)
canndat<-canres$FSTccscore
canndatf<-apply(canndat[, -1], 2, as.numeric)
dimnames(canndatf)[[1]]<-canndat[,1]
expr<-as.matrix(canndatf[, 1:(ncol(canndatf)/2)])
mtyl<-as.matrix(canndatf[, (ncol(canndatf)/2+1):ncol(canndatf)])
exprsetx<-new("ExpressionSet", exprs=expr, phenoData = pheDat)
exprsety<-new("ExpressionSet", exprs=mtyl, phenoData = pheDat)
PRres<-PROMISE2(exprSet=exprsetx, exprSet2=exprsety,
geneSet=NULL,
promise.pattern=promise.pattern,
strat.var=strat.var,
nperms=nperms,
nbperm=nbperm,
max.ntail=max.ntail,
seed=seed)$generes
if (is.null(prlbl ))
{prlbl<-c(promise.pattern[, 'endpt.vars'], paste('PR', nrow(promise.pattern), sep=""))}
if (!nbperm)
dimnames(PRres)[[2]]<-c('Gene', paste(paste(EMlbl[1], prlbl, sep="_"), 'Stat', sep="."),
paste(paste(EMlbl[2], prlbl, sep="_"), 'Stat', sep="."),
paste(prlbl[length(prlbl)], 'Stat', sep="."),
paste(paste(EMlbl[1], prlbl, sep="_"), 'Pval', sep="."),
paste(paste(EMlbl[2], prlbl, sep="_"), 'Pval', sep="."),
paste(prlbl[length(prlbl)], 'Pval', sep="."))
if (nbperm)
dimnames(PRres)[[2]]<-c('Gene', paste(paste(EMlbl[1], prlbl, sep="_"), 'Stat', sep="."),
paste(paste(EMlbl[2], prlbl, sep="_"), 'Stat', sep="."),
paste(prlbl[length(prlbl)], 'Stat', sep="."),
paste(paste(EMlbl[1], prlbl, sep="_"), 'Pval', sep="."),
paste(paste(EMlbl[2], prlbl, sep="_"), 'Pval', sep="."),
paste(prlbl[length(prlbl)], 'Pval', sep="."), 'nperm')
return(list(PRres=PRres, CCres=canres$CCres,
FSTccscore=canres$FSTccscore, CCload=canres$CCload))
}
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