missingGenotypeByScanChrom {GWASTools} | R Documentation

## Missing Counts per Scan per Chromosome

### Description

This function tabulates missing genotype calls for each scan for each chromosome.

### Usage

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

### Arguments

`genoData` | `GenotypeData` object. Chromosomes are expected to be in contiguous blocks.
`snp.exclude` | A vector of IDs corresponding to the SNPs that should be excluded from the overall missing count.
`verbose` | Logical value specifying whether to show progress information.

### Details

This function calculates the percent of missing genotypes in each chromosome of each scan 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," "snps.per.chr", and "missing.fraction."

`missing.counts` | A matrix with rows corresponding to the scans and columns indicating unique chromosomes containing the number of missing SNP's for each scan and chromosome.
`snps.per.chr` | A vector containing the number of non-excluded SNPs for each chromosome.
`missing.fraction` | A vector containing the fraction of missing counts for each scan over all chromosomes, excluding the Y chromosome for females.

### Author(s)

Cathy Laurie

### See Also

`GenotypeData`, `missingGenotypeBySnpSex`

### 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 <- missingGenotypeByScanChrom(genoData)
    close(genoData)

[Package GWASTools version 1.40.0 Index]