calculateMissingness: Calculate Missingness Proportions

Description Usage Arguments Value

Description

Calculates the proportion of missing data for each SNPs or each isolate where missing values are denoted by -1. Missing values are calculated for each column of genotypes (where columns are isolates and rows are SNPs), however genotypes can be transposed to calculate missingness proportions for SNPs.

Usage

1

Arguments

genotypes

An integer matrix of genotype data of the form -1, 0, 1 and 2 representing missing genotypes, homozygous reference, heterozygous and homozygous alternative respectively.

Value

A vector of length n where n is the number of columns in genotypes.


bahlolab/isoRelate documentation built on May 11, 2019, 5:25 p.m.