hlaAlleleToVCF: Convert HLA alleles to VCF

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Convert HLA alleles to VCF

Description

To convert the HLA allele data to a VCF file.

Usage

hlaAlleleToVCF(hla, outfn, DS=TRUE, allele.list=FALSE, prob.cutoff=NaN,
    verbose=TRUE)

Arguments

hla	an object of hlaAlleleClass for HLA alleles, or a list of hlaAlleleClass objects
outfn	a VCF file name or a connection; if outfn ends with ".gz" or ".xz", gzfile or xzfile will be used to compress the output file
DS	if TRUE, output dosages in the DS field
allele.list	a logical value or a character vector for a list of alleles; when it is a logical value, if TRUE and dosage is available, use all possible alleles in the dosages; otherwise, use the alleles predicted at least once
prob.cutoff	a probability threshold for setting the output alleles and dosages to missing; the output VCF file contains all samples in hla ignoring prob.cutoff
verbose	if TRUE, show information

Value

Return outfn.

Author(s)

Xiuwen Zheng

References

Zheng X, Shen J, Cox C, Wakefield J, Ehm M, Nelson M, Weir BS; HIBAG – HLA Genotype Imputation with Attribute Bagging. Pharmacogenomics Journal. doi: 10.1038/tpj.2013.18. https://www.nature.com/articles/tpj201318

See Also

hlaAttrBagging, hlaAllele

Examples

# make a "hlaAlleleClass" object
hla.id <- "A"
hla <- hlaAllele(HLA_Type_Table$sample.id,
    H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")],
    H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")],
    locus=hla.id, assembly="hg19")

# SNP predictors within the flanking region on each side
region <- 500   # kb
snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position,
    hla.id, region*1000, assembly="hg19")
length(snpid)  # 275

# train a HIBAG model
set.seed(100)
# please use "nclassifier=100" when you use HIBAG for real data
model <- hlaAttrBagging(hla, HapMap_CEU_Geno, nclassifier=2)
summary(model)

# validation
pred <- hlaPredict(model, HapMap_CEU_Geno)
summary(pred)


# output to standard output with dosages
hlaAlleleToVCF(hlaAlleleSubset(pred, 1:4), stdout())

zhengxwen/HIBAG documentation built on April 16, 2024, 8:41 a.m.