homoZygotTest {detectRUNS}

Function to check whether a window is (loosely) homozygous or not

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