hlaGenoSubset: Get a subset of genotypes
In HIBAG: HIBAG -- HLA Genotype Imputation with Attribute Bagging

Description Usage Arguments Details Value Author(s) See Also Examples

To get a subset of genotypes from a hlaSNPGenoClass object.

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

`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

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).

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”

Xiuwen Zheng

hlaMakeSNPGeno, hlaMakeSNPHaplo, hlaHaploSubset, hlaGenoCombine

# load SNP genotypes
data(HapMap_CEU_Geno, package="HIBAG")
summary(HapMap_CEU_Geno)

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