homoZygotTestCpp

vector of 0/1 genotypes (from genoConvert())

vector of differences between consecutive positions (gaps) in bps

gaps

max n. of heterozygous SNP in a homozygous window

maxHet

maxMiss

max distance between consecutive SNP in a window to be still considered a potential run

maxGap

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

Detection of runs of homozygosity and of heterozygosity
in diploid genomes using two methods: sliding windows (Purcell et al (2007)
<doi:10.1086/519795>) and consecutive runs (Marras et al (2015)
<doi:10.1111/age.12259>).

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

Description

Usage

Arguments

Value