hlaSNPGenoClass: The class of SNP genotypes

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

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 NA for missing values (other values have no meaning)
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”; B is usually defined as a major or reference allele, while A is defined as a minor or alternative allele
assembly	the human genome reference, such like "hg19"

Author(s)

Xiuwen Zheng

See Also

hlaMakeSNPGeno

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