tableRuns: Function to retrieve most common runs in the population

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

Description

This function takes in input either the run results or the output from the function snpInsideRuns (proportion of times a SNP is inside a run) in the population/group, and returns a subset of the runs most commonly found in the group/population. The parameter threshold controls the definition of most common (e.g. in at least 50%, 70% etc. of the sampled individuals)

Usage

tableRuns(runs = NULL, SnpInRuns = NULL, genotypeFile, mapFile,
  threshold = 0.5)

Arguments

runs	R object (dataframe) with results on detected runs
SnpInRuns	dataframe with the proportion of times each SNP falls inside a run in the population (output from snpInsideRuns)
genotypeFile	Plink ped file (for SNP position)
mapFile	Plink map file (for SNP position)
threshold	value from 0 to 1 (default 0.7) that controls the desired proportion of individuals carrying that run (e.g. 70%)

Value

A dataframe with the most common runs detected in the sampled individuals (the group/population, start and end position of the run, chromosome and number of SNP included in the run are reported in the output dataframe)

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')

tableRuns(runs = runsDF, genotypeFile = genotypeFile, mapFile = mapFile, threshold = 0.5)

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