homoZygotTestCpp: 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

homoZygotTestCpp(x, gaps, maxHet, maxMiss, maxGap)

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

Value

TRUE/FALSE (whether a window is homozygous or NOT)

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