detectRUNS is a R package for the detection of runs of homozygosity (ROH/ROHom) and of heterozygosity (ROHet, a.k.a. "heterozygosity-rich regions") in diploid genomes. Besides runs detection, it implements several functions to summarize and plot results.
detectRUNS is installed as a standard R package. Some core functions are written in C++ to increase efficieny of calculations: this makes use of the R library Rcpp. detectRUNS uses other R packages for data manipulation and plots. These packages are set as Imports, and detectRUNS will try to install any missing packages upon installation.
detectRUNS imports: plyr, iterators, itertools, ggplot2, reshape2, Rcpp, gridExtra, data.table detectRUNS suggests: testthat, knitr, rmarkdown, prettydoc
Please see the package vignette for a complete tutorial. What follows is a minimal working example to give the gist of the tool.
This is a basic example which shows you how to detect runs of homozygosity (ROH):
#1) detectRUNS (sliding-windows method)
genotypeFile <- system.file("extdata", "Kijas2016_Sheep_subset.ped", package = "detectRUNS")
mapFile <- system.file("extdata", "Kijas2016_Sheep_subset.map", package = "detectRUNS")
# calculating runs with sliding window approach
\dontrun{
# skipping runs calculation
runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1,
minSNP = 15, ROHet = FALSE, maxOppWindow = 1, maxMissWindow = 1, maxGap=10^6,
minLengthBps = 100000, minDensity = 1/10000)
}
# loading pre-calculated data
runsFile <- system.file("extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
colClasses <- c(rep("character", 3), rep("numeric", 4) )
runs <- read.csv2(runsFile, header = TRUE, stringsAsFactors = FALSE, colClasses = colClasses)
#2) summarise results
summaryList <- summaryRuns(runs = runs, mapFile = mapFilePath, genotypeFile = genotypeFilePath, Class = 6, snpInRuns = TRUE)
#3) plot results
plot_Runs(runs = runs)