getCQCg <-
function(DList=NULL,colLabel=NULL,overlapGenes=TRUE,filterGenes=F,cutRatioByMean=0.1, cutRatioByVar=0.1){
# DList - a list of studies
# overlapGenes - get the overlap genes among studies
# filterGenes - meta filter gene or not
# cutRatioByMean - meta mean filter ratio
# cutRatioByVar - meta var filter ratio
# pvalAdjustGene - adjust p-value or not for DE gene
# check DList
if(is.null(DList)){
stop("Error: DList is a required argument.")
}
K=length(DList)
if(K<3){
stop("Error: Insufficient number of studies.")
}
# check colLabel
if(is.null(colLabel)){
stop("Error: colLabel is a required argument.")
}
if(length(colLabel)!=K){
stop("Error: Unequal length of DList and colLabel")
}
for(k in 1:K){
if(prod(colLabel[[k]]%in%c(0,1))==F){
stop(paste("Error: colLabel for study ",k," has to be either 0 or 1 ."))
}
}
# get overlap genes
if(overlapGenes){
DList=metaOverlap(DList)
}
# filter genes
if(filterGenes){
DList=metaFilterData(DList,cutRatioByMean, cutRatioByVar)
}
# calculate CQCg
G=nrow(DList[[1]])
CQCg=rep(0,times=K)
for(k in 1:K){
# single
pSingle=DEsingle(DList[[k]],colLabel[[k]],pvalAdjust=FALSE,method="t")
rankSingle=rank(pSingle)
# meta
pMeta=DEmeta(DList[-k],colLabel[-k],pvalAdjust=FALSE,method="t")
rankMeta=rank(pMeta)
# test
rho=1-6*sum((rankSingle-rankMeta)^2)/G/(G^2-1) ## --> problematic here, maybe minus value
if(rho<=-1){
print("Warining, rho<=-1, invalide testing")
CQCp[k]=0
}else if(rho>=1){
print("Warining, rho>=1, invalide testing")
CQCp[k]=0
}else{
tValue=rho*sqrt((G-2)/(1-rho^2))
#pValue=1-pt(tValue,df=(G-2))
pValue=pt(-tValue,df=(G-2))
CQCg[k]=-log(pValue)
}
} # end k
# correction
CQCg[which(CQCg==Inf)]=410
names(CQCg)=names(DList)
return(CQCg)
}
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