createRUNdf

vector of TRUE/FALSE (is the SNP in a RUN?)

snpRun

mapFile

minSNP

minimum length of run in bps (defaults to 1000 bps = 1 kbps)

minLengthBps

minimum n. of SNP per kbps (defaults to 0.1 = 1 SNP every 10 kbps)

minDensity

indexed array of missing and opposite genotypes (SNP order in the genome is the index)

oppositeAndMissingSNP

max n. of opposite genotype SNPs in the run (not in the window!)

maxOppRun

max n. of missing SNPs in the run (not in the window!)

maxMissRun

Function to create a dataframe of RUNS per individual animal
Requires a map file (other filename to read or R object)
Parameters on maximum number of missing and opposite genotypes in the run (not the window) are implemented here

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>).

Filippo Biscarini

detectRUNS

Detect Runs of Homozygosity and Runs of Heterozygosity in
Diploid Genomes

Paolo Cozzi

Giustino Gaspa

Gabriele Marras

createRUNdf function

Function to create a dataframe of RUNS per individual animal
Requires a map file (other filename to read or R object)
Parameters on maximum number of missing and opposite genotypes in the run (not the window) are implemented here — createRUNdf

Function to create a dataframe of RUNS per individual animal
Requires a map file (other filename to read or R object)
Parameters on maximum number of missing and opposite genotypes in the run (not the window) are implemented here

createRUNdf: Function to create a dataframe of RUNS per individual animal Requires a map file (other filename to read or R object) Parameters on maximum number of missing and opposite genotypes in the run (not the window) are implemented here

Description

Usage

Arguments

Value