Nothing
.combine.Models <- function(reference.fn,target.fn,out.dir,verbose)
{
snpgdsCombineGeno(c(target.fn,reference.fn),
file.path(out.dir,"Aggregated.gds"),
method = 'position',
verbose=verbose,
snpfirstdim = TRUE)
if(file.exists(file.path(out.dir,"Aggregated.gds")))
{
# ancestry DataFrame have to be manually combined into aggregated model
genofile <- snpgdsOpen(file.path(out.dir,"Aggregated.gds"),readonly = F)
target.model = snpgdsOpen(target.fn)
target.sample.annot = read.gdsn(index.gdsn(target.model,'sample.annot'))
# target.sign = paste(read.gdsn(index.gdsn(target.model,'snp.chromosome')),read.gdsn(index.gdsn(target.model,'snp.position')),sep=":")
reference.model = snpgdsOpen(reference.fn)
reference.sample.annot = read.gdsn(index.gdsn(reference.model,'sample.annot'))
# reference.sign = paste(read.gdsn(index.gdsn(reference.model,'snp.chromosome')),read.gdsn(index.gdsn(reference.model,'snp.position')),sep=":")
# ref.idx = reference.sign%in%target.sign
# snp.ref = read.gdsn(index.gdsn(reference.model,'snp.ref'))[ref.idx]
# snp.alt = read.gdsn(index.gdsn(reference.model,'snp.alt'))[ref.idx]
sample.annot <- rbind(target.sample.annot,reference.sample.annot)
add.gdsn(genofile,"sample.annot",sample.annot)
# add.gdsn(genofile,"snp.ref",snp.ref)
# add.gdsn(genofile,"snp.alt",snp.alt)
snpgdsClose(genofile)
snpgdsClose(target.model)
snpgdsClose(reference.model)
return(TRUE)
} else
{
return(FALSE)
}
}
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