hlaMakeSNPHaplo: Make a SNP haplotype object

In HIBAG: HIBAG -- HLA Genotype Imputation with Attribute Bagging

Description

To create a hlaSNPHaploClass object (SNP haplotypic object).

Usage

hlaMakeSNPHaplo(haplotype, sample.id, snp.id, snp.position,
	A.allele, B.allele, assembly=c("auto", "hg18", "hg19", "unknown"))

Arguments

haplotype	a haplotype matrix, “# of SNPs” - by - “2 x # of individuals”
sample.id	a vector of sample ids
snp.id	a vector of SNP ids
snp.position	a vector of SNP positions
A.allele	a vector of A alleles in the SNP list
B.allele	a vector of B alleles in the SNP list
assembly	the human genome reference: "hg19" (default), "hg18", "auto" refers to "hg19"

Details

haplotype is a numeric matrix, with an entry value 0 standing for B (ZERO A allele), 1 for A (ONE A allele) and others for missing values (missing genotypes are usually set to be NA).

Value

Return a hlaSNPHaploClass object, and it is a list:

haplotype	a haplotype matrix, “# of SNPs” - by - “2 x # of individuals”
sample.id	a vector of sample IDs
snp.id	a vector of SNP IDs
snp.position	a vector of SNP positions in basepair
snp.allele	a vector of characters with the format of “A allele/B allele”
assembly	the human genome reference

Author(s)

Xiuwen Zheng

See Also

hlaMakeSNPGeno, hlaGenoSubset, hlaHaploSubset

HIBAG documentation built on May 2, 2019, 4:50 p.m.