calcFreqMissSnpGenosPerSnp: Missing genotypes
In timflutre/rutilstimflutre: Timothee Flutre's personal R code

calcFreqMissSnpGenosPerSnp

R Documentation

Missing genotypes

Description

Calculate the frequency of missing genotypes for each marker.

Usage

calcFreqMissSnpGenosPerSnp(X = NULL, vcf.file = NULL, yieldSize = 10000)

Arguments

`X`	matrix of marker genotypes, with genotypes in rows and markers in columns; missing values should be encoded as NA; if not NULL, will be used in priority even if `vcf.file` is not NULL
`vcf.file`	path to the VCF file (if the bgzip index doesn't exist in the same directory, it will be created); used only if `X=NULL`
`yieldSize`	number of records to yield each time the VCF file is read from (see ?TabixFile)

Value

vector

Author(s)

Timothee Flutre

Examples

## Not run: ## simulate fake SNP genotypes
set.seed(1859)
X <- simulGenosDose(nb.genos=200, nb.snps=10^3)

## randomly create missing SNP genotypes
idx <- sample.int(n=length(X), size=10^3)
X[idx] <- NA

miss.snp <- calcFreqMissSnpGenosPerSnp(X=X)
hist(miss.snp, xlab="proportion of missing data at a given SNP,\nmeasured across all individuals", ylab="number of SNPs")

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.