hetByScanChrom: Heterozygosity rates by scan and chromosome

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

Description

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

Usage

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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

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


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