hlaGenoSubset: Get a subset of genotypes

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Get a subset of genotypes

Description

To get a subset of genotypes from a hlaSNPGenoClass object.

Usage

hlaGenoSubset(genoobj, samp.sel=NULL, snp.sel=NULL, snp.id=NULL)

Arguments

genoobj	a genotype object of hlaSNPGenoClass
samp.sel	a logical vector, or an integer vector of indices
snp.sel	a logical vector, or an integer vector of indices
snp.id	SNP IDs to be selected, or NULL

Details

genoobj$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	optional, human genome information

Author(s)

Xiuwen Zheng

See Also

hlaMakeSNPGeno, hlaGenoCombine

Examples

summary(HapMap_CEU_Geno)

geno <- hlaGenoSubset(HapMap_CEU_Geno,
    snp.sel = (hlaGenoMFreq(HapMap_CEU_Geno)>0.10))
summary(geno)

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