slidingRuns: Function to detect runs using sliding window approach

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

Description

This is a core function not intended to be exported

Usage

slidingRuns(indGeno, individual, mapFile, gaps, parameters, cpp = TRUE)

Arguments

indGeno	vector of 0/1/NAs of individual genotypes (0: homozygote; 1: heterozygote)
individual	list of group (breed, population, case/control etc.) and ID of individual sample
mapFile	Plink map file (for SNP position)
gaps	distance between SNPs
parameters	list of parameters
cpp	use cpp functions or not (DEBUG)

Details

This method uses sliding windows to detect RUNs. Checks on minimum n. of SNP, max n. of opposite and missing genotypes, max gap between adjacent loci and minimum length of the run are implemented (as in the sliding window method). Both runs of homozygosity (RoHom) and of heterozygosity (RoHet) can be search for (option ROHet: TRUE/FALSE) NOTE: this methods is intended to not be exported

Value

A data frame of runs per individual sample

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