HIBAG (version 1.8.3)

hlaMakeSNPGeno: 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 in the SNP list

B.allele

a vector of B alleles in the SNP list

assembly

the human genome reference: "hg18", "hg19" (default), "hg20"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning

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

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).

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)