Package: detectRUNS 0.9.6.9000

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]

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detectRUNS.pdf |detectRUNS.html✨
detectRUNS/json (API)
NEWS

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

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

16 exports 8 stars 2.87 score 37 dependencies 11 mentions 31 scripts 365 downloads

Last updated 2 years agofrom:e383906cf1. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 21 2024
R-4.5-win-x86_64OKAug 21 2024
R-4.5-linux-x86_64OKAug 21 2024
R-4.4-win-x86_64OKAug 21 2024
R-4.4-mac-x86_64OKAug 21 2024
R-4.4-mac-aarch64OKAug 21 2024
R-4.3-win-x86_64OKAug 21 2024
R-4.3-mac-x86_64OKAug 21 2024
R-4.3-mac-aarch64OKAug 21 2024

Exports:consecutiveRUNS.runFroh_inbreedingFroh_inbreedingClassplot_DistributionRunsplot_InbreedingChrplot_manhattanRunsplot_PatternRunsplot_Runsplot_SnpsInRunsplot_StackedRunsplot_ViolinRunsreadExternalRunsreorderDFslidingRUNS.runsummaryRunstableRuns

Dependencies:clicolorspacedata.tablefansifarverggplot2gluegridExtragtableisobanditeratorsitertoolslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr

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

Filippo Biscarini, Paolo Cozzi, Giustino Gaspa, Gabriele Marras

Rendered fromdetectRUNS.vignette.Rmdusingknitr::rmarkdownon Aug 21 2024.

Last update: 2018-02-02
Started: 2017-11-08

Readme and manuals

Help Manual

Help pageTopics
Main function to detect genomic RUNS (ROHom/ROHet) using the consecutive methodconsecutiveRUNS.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 herecreateRUNdf
Function to calculate oppositeAndMissingGenotypes arrayfindOppositeAndMissing
Function to calculated Froh genome-wide or chromosome-wideFroh_inbreeding
Function to calculated Froh using a ROH-classFroh_inbreedingClass
Convert 0/1/2 genotypes to 0/1genoConvertCpp
Function to check whether a window is (loosely) heterozygous or notheteroZygotTest
Function to check whether a window is (loosely) heterozygous or notheteroZygotTestCpp
Function to check whether a window is (loosely) homozygous or nothomoZygotTest
Function to check whether a window is (loosely) homozygous or nothomoZygotTestCpp
Convert ped genotypes to 0/1pedConvertCpp
Plot Distribution of runsplot_DistributionRuns
Plot Froh-based inbreeding coefficients by groupplot_InbreedingChr
Plot the proportion of times SNPs are inside runs - MANHATTAN PLOTplot_manhattanRuns
Plot sum of run-lengths (or average run-lengths) against the number of runs per individualplot_PatternRuns
Function to plot runs per individualplot_Runs
Plot the number of times each SNP falls inside runsplot_SnpsInRuns
Plot stacked runsplot_StackedRuns
Violin plot of run length per individual (either sum or mean)plot_ViolinRuns
Read runs from external filesreadExternalRuns
Function to return a dataframe of population (POP, ID)readPOPCpp
Function to reorder data frames by CHROMOSOMEreorderDF
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 RUNsnpInRun
Function to return a vector of T/F for whether a SNP is or not in a RUNsnpInRunCpp
Function to count number of times a SNP is in a RUNsnpInsideRunsCpp
Summary statistics on detected runssummaryRuns
Function to retrieve most common runs in the populationtableRuns
Function to write out RUNS per individual animalwriteRUN