Package: detectRUNS 0.9.7

Filippo Biscarini

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

Detection of runs of homozygosity and of heterozygosity in diploid genomes using two methods: sliding windows (Purcell et al (2007) <doi:10.1086/519795>) and consecutive runs (Marras et al (2015) <doi:10.1111/age.12259>).

Authors:Filippo Biscarini [aut, cre], Paolo Cozzi [aut], Giustino Gaspa [aut], Gabriele Marras [aut]

detectRUNS_0.9.7.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
detectRUNS/json (API)

# Install 'detectRUNS' in R:

install.packages('detectRUNS', repos = c('https://bioinformatics-ptp.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioinformatics-ptp/detectruns/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

7.61 score 14 stars 65 scripts 423 downloads 11 mentions 16 exports 27 dependencies

Last updated from:0265c4d58c. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	176
linux-devel-x86_64	OK	165
source / vignettes	OK	220
linux-release-arm64	OK	202
linux-release-x86_64	OK	162
macos-release-arm64	OK	154
macos-release-x86_64	OK	244
macos-oldrel-arm64	OK	121
macos-oldrel-x86_64	OK	261
windows-devel	OK	151
windows-release	OK	146
windows-oldrel	OK	161
wasm-release	OK	119

Exports:consecutiveRUNS.run Froh_inbreeding Froh_inbreedingClass plot_DistributionRuns plot_InbreedingChr plot_manhattanRuns plot_PatternRuns plot_Runs plot_SnpsInRuns plot_StackedRuns plot_ViolinRuns readExternalRuns reorderDF slidingRUNS.run summaryRuns tableRuns

Dependencies:cli cpp11 data.table farver ggplot2 glue gridExtra gtable isoband iterators itertools labeling lifecycle magrittr plyr R6 RColorBrewer Rcpp reshape2 rlang S7 scales stringi stringr vctrs viridisLite withr

detectRUNS: an R package to detect runs of homozygosity and heterozygosity in diploid genomes

Overview | Sample data | Detect runs | sliding-window-based run detection | consecutive SNP-based run detection | "Runs of heterozygosity" (a.k.a. heterozygosity-rich regions) | Summary statistics on detected runs | Plots | $F_{ROH}$: ROH-based inbreeding | Importing data from external files | References

Rendered fromdetectRUNS.vignette.Rmdusingknitr::rmarkdown

Last update: 2026-05-28
Started: 2017-11-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Classify runs in bins.	classifyRuns
Main function to detect genomic RUNS (ROHom/ROHet) using the consecutive method	consecutiveRUNS.run
Function to detect consecutive runs in a vector (individual's genotypes)	consecutiveRunsCpp
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	createRUNdf
Function to calculate oppositeAndMissingGenotypes array	findOppositeAndMissing
Function to calculated Froh genome-wide or chromosome-wide	Froh_inbreeding
Function to calculated Froh using a ROH-class	Froh_inbreedingClass
Convert 0/1/2 genotypes to 0/1	genoConvertCpp
Function to check whether a window is (loosely) heterozygous or not	heteroZygotTest
Function to check whether a window is (loosely) heterozygous or not	heteroZygotTestCpp
Function to check whether a window is (loosely) homozygous or not	homoZygotTest
Function to check whether a window is (loosely) homozygous or not	homoZygotTestCpp
Convert ped genotypes to 0/1	pedConvertCpp
Plot Distribution of runs	plot_DistributionRuns
Plot Froh-based inbreeding coefficients by group	plot_InbreedingChr
Plot the proportion of times SNPs are inside runs - MANHATTAN PLOT	plot_manhattanRuns
Plot sum of run-lengths (or average run-lengths) against the number of runs per individual	plot_PatternRuns
Function to plot runs per individual	plot_Runs
Plot the number of times each SNP falls inside runs	plot_SnpsInRuns
Plot stacked runs	plot_StackedRuns
Violin plot of run length per individual (either sum or mean)	plot_ViolinRuns
Read runs from external files	readExternalRuns
Function to return a dataframe of population (POP, ID)	readPOPCpp
Function to reorder data frames by CHROMOSOME	reorderDF
Main function to detect RUNS (ROHom/ROHet) using sliding windows (a la Plink)	slidingRUNS.run
Function to slide a window over a vector (individual's genotypes)	slidingWindow
Function to slide a window over a vector (individual's genotypes)	slidingWindowCpp
Function to return a vector of T/F for whether a SNP is or not in a RUN	snpInRun
Function to return a vector of T/F for whether a SNP is or not in a RUN	snpInRunCpp
Function to count number of times a SNP is in a RUN	snpInsideRunsCpp
Summary statistics on detected runs	summaryRuns
Function to retrieve most common runs in the population	tableRuns
Function to write out RUNS per individual animal	writeRUN