detectRUNS is a R package for the detection of runs of homozygosity(ROH/ROHom) and of heterozygosity (ROHet, a.k.a. “heterozygosity-richregions”) in diploid genomes. Besides runs detection, it implementsseveral functions to summarize and plot results.
detectRUNS is installed as a standard R package. Some core functionsare written in C++ to increase efficieny of calculations: this makes useof the R library Rcpp. detectRUNS uses other R packages for datamanipulation and plots. These packages are set asImports, anddetectRUNS will try to install any missing packages uponinstallation.
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 followsis a minimal working example to give the gist of the tool.
This is a basic example which shows you how to detect runs ofhomozygosity (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 datarunsFile<-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 resultssummaryList<-summaryRuns(runs = runs,mapFile = mapFilePath,genotypeFile = genotypeFilePath,Class =6,snpInRuns =TRUE)#3) plot resultsplot_Runs(runs = runs)