consecutiveRuns: Function to detect consecutive runs in a vector (individual's...

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

Description

This is a core function. It implements the consecutive method for detection of runs in diploid genomes (see Marras et al. 2015)

Usage

consecutiveRuns(indGeno, individual, mapFile, ROHet = TRUE, minSNP = 3,
  maxOppositeGenotype = 1, maxMiss = 1, minLengthBps = 1000,
  maxGap = 10^6)

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)
ROHet	shall we detect ROHet or ROHom?
minSNP	minimum number of SNP in a run
maxOppositeGenotype	max n. of homozygous/heterozygous SNP
maxMiss	max. n. of missing SNP
minLengthBps	min length of a run in bps
maxGap	max distance between consecutive SNP in a window to be still considered a potential run

Details

The consecutive method detect runs by consecutively scanning SNP loci along the genome. No sliding windows are used. 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)

Value

A data frame of runs per individual sample

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