Nothing
.create.Target.Model <-function(sample.names,genotype.dir,out.dir,cores,bam.chr.encoding)
{
files = list.files(genotype.dir,"genotype.vcf")
files = files[which(files%in%paste(sample.names,".genotype.vcf",sep=""))]
geno = fread(paste(genotype.dir,files[1],sep=""),sep="\t",header=T,data.table=FALSE,showProgress = F,skip="#CHROM")
res = mclapply(files,function(f)
{
geno = fread(paste(genotype.dir,f,sep=""),sep="\t",header=T,data.table=TRUE,showProgress=F,skip="#CHROM")
geno[,10]
},mc.cores=cores)
vcf = cbind(geno[,1:9],data.frame(do.call(cbind,res)))
vcf[,1] = gsub("chr","",as.character(vcf[,1]))
snp.allele = rep("A/B",nrow(vcf))
.convertGeno(vcf,snp.allele)
vcf.info = vcf[,1:9]
sample.id = colnames(vcf)[10:ncol(vcf)]
vcf = as.matrix(vcf[,10:ncol(vcf)])
mode(vcf) = "integer"
snpgdsCreateGeno(file.path(out.dir,"Target.gds"),
genmat = vcf,
sample.id = sample.id,
snp.id = paste(vcf.info[,1],vcf.info[,2],vcf.info[,3],sep=":"),
snp.rs.id = vcf.info[,3],
snp.chromosome = vcf.info[,1],
snp.position = vcf.info[,2],
snp.allele = snp.allele,
snpfirstdim=TRUE)
genofile <- snpgdsOpen(file.path(out.dir,"Target.gds"),readonly = F)
sample.annot <- data.frame(pop.group=rep("ND",ncol(vcf)),sex=rep("M",ncol(vcf)))
add.gdsn(genofile,"sample.annot",sample.annot)
add.gdsn(genofile,"snp.ref",vcf.info[,4])
add.gdsn(genofile,"snp.alt",vcf.info[,5])
snpgdsClose(genofile)
}
.create.Target.Model.From.VCF <- function(vcf.fn,out.dir,cores)
{
vcf = fread(vcf.fn,sep="\t",data.table=FALSE,showProgress=FALSE,skip="#CHROM")
### Chromosomes without chr encoding
vcf[,1] = gsub("chr","",as.character(vcf[,1]))
snp.allele = rep("A/B",nrow(vcf))
.convertGeno(vcf,snp.allele)
vcf.info = vcf[,1:9]
sample.id = colnames(vcf)[10:ncol(vcf)]
vcf = as.matrix(vcf[,10:ncol(vcf)])
mode(vcf) = "integer"
snpgdsCreateGeno(file.path(out.dir,"Target.gds"),
genmat = vcf,
sample.id = sample.id,
snp.id = paste(vcf.info[,1],vcf.info[,2],vcf.info[,3],sep=":"),
snp.rs.id = vcf.info[,3],
snp.chromosome = vcf.info[,1],
snp.position = vcf.info[,2],
snp.allele = snp.allele,
snpfirstdim=TRUE)
genofile <- snpgdsOpen(file.path(out.dir,"Target.gds"),readonly = F)
sample.annot <- data.frame(pop.group=rep("ND",ncol(vcf)),sex=rep("M",ncol(vcf)))
add.gdsn(genofile,"sample.annot",sample.annot)
add.gdsn(genofile,"snp.ref",vcf.info[,4])
add.gdsn(genofile,"snp.alt",vcf.info[,5])
snpgdsClose(genofile)
}
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