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#source("/Users/yujiang/Research/compound_heterozygosity/for_R_package_temp/compHet_TDT_single.R")
coreTDT_single = function(ped,maf.threshold=1,qc.proportion=0.8,geneid=NA,control.maf=NULL){
nfamily = dim(ped)[1]/3
nsnp = dim(ped)[2]
##variants selection based on maf in evs
if(nsnp < 1){
cat(geneid,nsnp,NA,NA,NA,NA,NA,NA,NA,NA,"\n")
return(NULL)
}
##check the coverage information
coverage_infor = apply(ped,2,function(x) mean(apply(matrix(x,ncol=3),1,function(y) any(is.na(y)))))
var_select = which(coverage_infor <= (1-qc.proportion))
#var_select = c(1:nsnp)
nsnp_select = length(var_select)
#cat("nsnp_select: ",nsnp_select,"\n")
child.geno.select1 =as.matrix(ped[1:nfamily,var_select])
parent.geno.select1 = array(NA,dim=c(nfamily,nsnp_select,2))
parent.geno.select1[1:nfamily,1:nsnp_select,1] = as.matrix(ped[(nfamily+1):(2*nfamily),var_select])
parent.geno.select1[1:nfamily,1:nsnp_select,2] =as.matrix(ped[(2*nfamily+1):(3*nfamily),var_select])
if(is.null(control.maf)){
parent_maf = apply(parent.geno.select1,2,function(x) (0.5 * mean(x,na.rm=T)))
var_select2 = which(parent_maf <= maf.threshold)
}else{
var_select2 = which(control.maf[var_select] <= maf.threshold)
}
nsnp_select2 = length(var_select2)
#cat("nsnp_select2: ",nsnp_select2,"\n")
if(nsnp_select2 < 1){
cat(geneid,nsnp_select2,NA,NA,NA,NA,NA,NA,NA,NA,"\n")
return(NULL)
}
child.geno.select2 =array(NA,dim=c(nfamily,nsnp_select2))
parent.geno.select2 = array(NA,dim=c(nfamily,nsnp_select2,2))
child.geno.select2[1:nfamily,1:nsnp_select2] = child.geno.select1[,var_select2]
parent.geno.select2[1:nfamily,1:nsnp_select2,1] = parent.geno.select1[,var_select2,1]
parent.geno.select2[1:nfamily,1:nsnp_select2,2] = parent.geno.select1[,var_select2,2]
##compute the p values
result = compHet_TDT_v6(parent.geno.select2,child.geno.select2)
return(result)
}
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