Froh_inbreedingClass: Function to calculated Froh using a ROH-class

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

Description

This function calculates the individual inbreeding coefficients based on runs of homozygosity (ROH) using only ROH of specific size classes. The parameter class specify the size interval to split up calculations. For example, if class = 2 Froh based on ROH 0-2, 2-4, 4-8, 80-16, >16 Mbps long will be calculated.

Usage

Froh_inbreedingClass(runs, mapFile, Class = 2)

Arguments

runs	R object (dataframe) with ROH results
mapFile	Plink map file (for SNP position)
Class	base ROH-length interval (in Mbps) (default: 0-2, 2-4, 4-8, 8-16, >16)

Value

A data frame with individual inbreeding coefficients based on ROH-length of specific size. The sum of ROH-length of specific size in each individual is reported alongside

Examples

# getting map and ped paths
genotypeFile <- system.file("extdata", "Kijas2016_Sheep_subset.ped", package = "detectRUNS")
mapFile <- system.file("extdata", "Kijas2016_Sheep_subset.map", package = "detectRUNS")

# calculating runs of Homozygosity
## Not run: 
# skipping runs calculation
runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1,  minSNP = 15,
ROHet = FALSE,  maxOppositeGenotype = 1, maxMiss = 1,  minLengthBps = 100000,  minDensity = 1/10000)

## End(Not run)
# loading pre-calculated data
runsFile <- system.file("extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
runsDF <- readExternalRuns(inputFile = runsFile, program = 'detectRUNS')

Froh_inbreedingClass(runs = runsDF, mapFile = mapFile, Class = 2)

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