hlaMakeSNPGeno: Make a SNP genotype object

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Make a SNP genotype object

Description

To create a hlaSNPGenoClass object (SNP genotypic object).

Usage

hlaMakeSNPGeno(genotype, sample.id, snp.id, snp.position,
    A.allele, B.allele, assembly="auto")

Arguments

genotype	a genotype matrix, “# of SNPs” - by - “# 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, A is usually defined as a minor or alternative allele
B.allele	a vector of B alleles, B is usually defined as a major or reference allele
assembly	the human genome reference: "hg18", "hg19" (default), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning

Details

genotype is a numeric matrix, with an entry value 0 standing for BB (ZERO A allele), 1 for AB (ONE A allele), 2 for AA (TWO A alleles) and others for missing values (missing genotypes are usually set to be NA).

Value

Return a hlaSNPGenoClass object, and it is a list:

genotype	a genotype matrix, “# of SNPs” - by - “# 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

hlaGenoSubset, hlaGenoCombine

Examples

summary(HapMap_CEU_Geno)

allele <- strsplit(HapMap_CEU_Geno$snp.allele, "/")
A.allele <- sapply(allele, function(x) { x[1] })
B.allele <- sapply(allele, function(x) { x[2] })

geno <- hlaMakeSNPGeno(HapMap_CEU_Geno$genotype, HapMap_CEU_Geno$sample.id,
    HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position, A.allele, B.allele,
    assembly="hg19")

summary(geno)

zhengxwen/HIBAG documentation built on Nov. 24, 2024, 5:24 a.m.