countGenotype: Count genotype

In GA4GHshiny: Shiny application for interacting with GA4GH-based data servers

Description

Summarize a list of genotype data. Variant calls with no coverage (./.) do not enter in this count.

Usage

countGenotype(genotype)

Arguments

genotype

list of integer vectors of length 2.

Value

data.frame of 1 row containing the columns below.

• ref.homozygous reference homosygous (e.g. 0/0);

• alt.heterozygous alternate heterozygous (e.g. 0/1, 1/2);

• ref.homozygous reference homozygous (e.g. 1/1, 2/2);

• total the sum of the three previous columns.

Examples

countGenotype(genotype = list(c(0,0), c(0,1), c(1,2), c(1,1), c(2,2)))

GA4GHshiny documentation built on Nov. 8, 2020, 5:56 p.m.