missingGenotypeByScanChrom: Missing Counts per Scan per Chromosome
In amstilp/GWASTools: Tools for Genome Wide Association Studies

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

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

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

`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.

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.

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.

Cathy Laurie

GenotypeData, missingGenotypeBySnpSex

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)