hlaMakeSNPGeno {HIBAG} | R Documentation

## Make a SNP genotype object

### Description

To create a `hlaSNPGenoClass` object (SNP genotypic object).

### Usage

    hlaMakeSNPGeno(genotype, sample.id, snp.id, snp.position,
        A.allele, B.allele, assembly="auto")

### Arguments

`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
`A.allele` | a vector of A alleles in the SNP list
`B.allele` | a vector of B alleles in the SNP list
`assembly` | the human genome reference: "hg18", "hg19" (default), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning

### Details

`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` | the human genome reference

### Author(s)

Xiuwen Zheng

### See Also

`hlaGenoSubset`, `hlaGenoCombine`

### Examples

    summary(HapMap_CEU_Geno)

    allele <- strsplit(HapMap_CEU_Geno$snp.allele, "/")
    A.allele <- sapply(allele, function(x) { x[1] })
    B.allele <- sapply(allele, function(x) { x[2] })

    geno <- hlaMakeSNPGeno(HapMap_CEU_Geno$genotype, HapMap_CEU_Geno$sample.id,
        HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position, A.allele, B.allele,
        assembly="hg19")

    summary(geno)

[Package HIBAG version 1.22.0 Index]