homoZygotTest: Function to check whether a window is (loosely) homozygous or...

In detectRUNS: Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

Description

This is a core function. Parameters on how to consider a window homozygous are here (maxHet, maxMiss)

Usage

homoZygotTest(x, gaps, maxHet, maxMiss, maxGap, i, windowSize)

Arguments

x	vector of 0/1 genotypes (from genoConvert())
gaps	vector of differences between consecutive positions (gaps) in bps
maxHet	max n. of heterozygous SNP in a homozygous window
maxMiss	max n. of missing in a window
maxGap	max distance between consecutive SNP in a window to be still considered a potential run
i	index along the genome (genome-vector for each individual)
windowSize	size of window (n. of SNP)

Value

a list: i) TRUE/FALSE (whether a window is heterozygous or NOT); ii) indexes of "opposite and missing" genotype

detectRUNS documentation built on Oct. 30, 2019, 11:41 a.m.