hetByScanChrom: Heterozygosity rates by scan and chromosome

In GWASTools: Tools for Genome Wide Association Studies

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)

GWASTools documentation built on Nov. 8, 2020, 7:49 p.m.