consecutiveRunsCpp {detectRUNS}

Function to detect consecutive runs in a vector (individual's genotypes)

Description

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

Usage

consecutiveRunsCpp(indGeno, individual, mapFile, ROHet = TRUE,
  minSNP = 3L, maxOppositeGenotype = 1L, maxMiss = 1L,
  minLengthBps = 1000L, maxGap = 1000000L)

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