missingGenotypeBySnpSex {GWASTools} | R Documentation

## Missing Counts per SNP by Sex

### Description

For all SNPs for each sex tabulates missing SNP counts, allele counts and heterozygous counts.

### Usage

    missingGenotypeBySnpSex(genoData, scan.exclude = NULL,
                            verbose = TRUE)

### Arguments

`genoData` | `GenotypeData` object.
`scan.exclude` | A vector containing the scan numbers of scans that are to be excluded from the total scan list.
`verbose` | Logical value specifying whether to show progress information.

### Details

This function calculates the fraction of missing genotypes for males and females for each SNP given in `genoData`. A "sex" variable must be present in the scan annotation slot of `genoData`.

### Value

This function returns a list with three components: "missing.counts," "scans.per.sex," and "missing.fraction."

`missing.counts` | A matrix with one row per SNP and one column per sex containing the number of missing SNP counts for males and females, respectively.
`scans.per.sex` | A vector containing the number of males and females respectively.
`missing.fraction` | A vector containing the fraction of missing counts for each SNP, with females excluded for the Y chromosome.

### Author(s)

Cathy Laurie, Stephanie Gogarten

### See Also

`GenotypeData`, `missingGenotypeByScanChrom`

### Examples

    library(GWASdata)
    file <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
    gds <- GdsGenotypeReader(file)

    # need scan annotation with sex
    data(illuminaScanADF)
    genoData <-  GenotypeData(gds, scanAnnot=illuminaScanADF)

    missingRate <- missingGenotypeBySnpSex(genoData)
    close(genoData)

[Package GWASTools version 1.30.1 Index]