hlaSNPGenoClass {HIBAG}R Documentation

The class of SNP genotypes

Description

The class of SNP genotypes, and its instance is returned from hlaMakeSNPGeno.

Value

There are five components:

genotype

a genotype matrix, “# of SNPs”-by-“# of individuals”; 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)

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 a format of “A allele/B allele”

assembly

the human genome reference, such like "hg19"

Author(s)

Xiuwen Zheng

See Also

hlaMakeSNPGeno


[Package HIBAG version 1.26.1 Index]