hlaGenoSubset: Get a subset of genotypes

In HIBAG: HLA Genotype Imputation with Attribute Bagging

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)

Example output

HIBAG (HLA Genotype Imputation with Attribute Bagging)
Kernel Version: v1.3
Supported by Streaming SIMD Extensions (SSE2) [64-bit]
SNP genotypes: 
	60 samples X 1564 SNPs
	SNPs range from 25769023bp to 33421576bp on hg19
Missing rate per SNP:
	min: 0, max: 0.0666667, mean: 0.0651215, median: 0.0666667, sd: 0.00968287
Missing rate per sample:
	min: 0, max: 0.969949, mean: 0.0651215, median: 0.000639386, sd: 0.243737
Minor allele frequency:
	min: 0, max: 0.5, mean: 0.227582, median: 0.205357, sd: 0.1389
Allelic information:
A/C A/G C/T G/T 
136 655 632 141 
SNP genotypes: 
	60 samples X 1197 SNPs
	SNPs range from 25769023bp to 33421576bp on hg19
Missing rate per SNP:
	min: 0, max: 0.0666667, mean: 0.0657059, median: 0.0666667, sd: 0.00757446
Missing rate per sample:
	min: 0, max: 0.978279, mean: 0.0657059, median: 0.000835422, sd: 0.245786
Minor allele frequency:
	min: 0.101695, max: 0.5, mean: 0.278734, median: 0.267857, sd: 0.117338
Allelic information:
A/C A/G C/T G/T 
105 511 476 105 

HIBAG documentation built on March 24, 2021, 6 p.m.