hetByScanChrom {GWASTools} | R Documentation

## Heterozygosity rates by scan and chromosome

### Description

This function calculates the fraction of heterozygous genotypes for each chromosome for a set of scans.

### Usage

    hetByScanChrom(genoData, snp.exclude = NULL,
                   verbose = TRUE)

### Arguments

`genoData` | `GenotypeData` object. Chromosomes are expected to be in contiguous blocks.
`snp.exclude` | An integer vector containing the id's of SNPs to be excluded.
`verbose` | Logical value specifying whether to show progress information.

### Details

This function calculates the percent of heterozygous and missing genotypes in each chromosome of each scan given in `genoData`.

### Value

The result is a matrix containing the heterozygosity rates with scans as rows and chromosomes as columns, including a column "A" for all autosomes.

### Author(s)

Cathy Laurie

### See Also

`GenotypeData`, `hetBySnpSex`

### Examples

    file <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
    gds <- GdsGenotypeReader(file)
    genoData <- GenotypeData(gds)
    het <- hetByScanChrom(genoData)
    close(genoData)

[Package GWASTools version 1.40.0 Index]