hetByScanChrom: Heterozygosity rates by scan and chromosome
In amstilp/GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Value Author(s) See Also Examples

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

1 2	hetByScanChrom(genoData, snp.exclude = NULL, verbose = TRUE)

`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.

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

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

Cathy Laurie

GenotypeData, hetBySnpSex

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