createRUNdf: Function to create a dataframe of RUNS per individual animal...

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

Description

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

Usage

createRUNdf(snpRun, mapFile, minSNP = 3, minLengthBps = 1000,
  minDensity = 1/10, oppositeAndMissingSNP, maxOppRun = NULL,
  maxMissRun = NULL)

Arguments

snpRun	vector of TRUE/FALSE (is the SNP in a RUN?)
mapFile	Plink-like map file (data.frame)
minSNP	minimum n. of SNP to call a RUN
minLengthBps	minimum length of run in bps (defaults to 1000 bps = 1 kbps)
minDensity	minimum n. of SNP per kbps (defaults to 0.1 = 1 SNP every 10 kbps)
oppositeAndMissingSNP	indexed array of missing and opposite genotypes (SNP order in the genome is the index)
maxOppRun	max n. of opposite genotype SNPs in the run (not in the window!)
maxMissRun	max n. of missing SNPs in the run (not in the window!)

Value

a data.frame with RUNS per animal

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