Package: ibdsim2 2.1.2

Magnus Dehli Vigeland

ibdsim2: Simulation of Chromosomal Regions Shared by Family Members

Simulation of segments shared identical-by-descent (IBD) by pedigree members. Using sex specific recombination rates along the human genome (Halldorsson et al. (2019) <doi:10.1126/science.aau1043>), phased chromosomes are simulated for all pedigree members. Applications include calculation of realised relatedness coefficients and IBD segment distributions. 'ibdsim2' is part of the 'pedsuite' collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite', including a separate chapter on 'ibdsim2', is available in the book 'Pedigree analysis in R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising and comparing IBD distributions is available at <https://magnusdv.shinyapps.io/ibdsim2-shiny/>.

Authors:Magnus Dehli Vigeland [aut, cre]

ibdsim2_2.1.2.tar.gz
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ibdsim2_2.1.2.tgz(r-4.4-x86_64)ibdsim2_2.1.2.tgz(r-4.4-arm64)ibdsim2_2.1.2.tgz(r-4.3-x86_64)ibdsim2_2.1.2.tgz(r-4.3-arm64)
ibdsim2_2.1.2.tar.gz(r-4.5-noble)ibdsim2_2.1.2.tar.gz(r-4.4-noble)
ibdsim2_2.1.2.tgz(r-4.4-emscripten)ibdsim2_2.1.2.tgz(r-4.3-emscripten)
ibdsim2.pdf |ibdsim2.html✨
ibdsim2/json (API)
NEWS

# Install 'ibdsim2' in R:
install.packages('ibdsim2', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/magnusdv/ibdsim2/issues

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

On CRAN:

identity-by-descentrelatednesssimulation

28 exports 5 stars 1.67 score 40 dependencies 1 dependents 16 scripts 585 downloads

Last updated 10 days agofrom:c4c30ab954. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 08 2024
R-4.5-win-x86_64OKSep 08 2024
R-4.5-linux-x86_64OKSep 08 2024
R-4.4-win-x86_64OKSep 08 2024
R-4.4-mac-x86_64OKSep 08 2024
R-4.4-mac-aarch64OKSep 08 2024
R-4.3-win-x86_64OKSep 08 2024
R-4.3-mac-x86_64OKSep 08 2024
R-4.3-mac-aarch64OKSep 08 2024

Exports:convertPoscustomMapestimateIdentityestimateInbreedingestimateKappaestimateKinshipestimateTwoLocusIdentityestimateTwoLocusInbreedingestimateTwoLocusKappaestimateTwoLocusKinshipextractIdsfindPatternhaploDrawibdsimkaryoHaploidlaunchApploadMapmapLenphysRangeplotSegmentDistributionprofileSimIBDrealisedIdentityrealisedInbreedingrealisedKapparealisedKinshipsegmentStatsuniformMapzeroIBD

Dependencies:clicolorspaceevaluatefansifarverggplot2gluegtablehighrisobandkinship2knitrlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepedmutpedtoolspillarpkgconfigquadprogR6RColorBrewerRcppribdrlangscalesslamtibbleutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Conversion of genetic map positionsconvertPos
Custom recombination mapcustomMap
Estimation of one- and two-locus relatedness coefficientsestimateCoeffs estimateIdentity estimateInbreeding estimateKappa estimateKinship estimateTwoLocusIdentity estimateTwoLocusInbreeding estimateTwoLocusKappa estimateTwoLocusKinship
Extract ID labels from simulation outputextractIds
Find specific IBD patternsfindPattern
Draw haplotypes onto a pedigree plothaploDraw
IBD simulationibdsim
Diploid karyogramkaryoDiploid
Karyogram plotskaryogram2
Haploid karyogramkaryoHaploid
Launch the ibdsim2 applaunchApp
Load a built-in genetic maploadMap
Physical and genetic map lengthsmapLen mapLen.chromMap mapLen.genomeMap maplengths physRange physRange.chromMap physRange.genomeMap
Scatter plots of IBD segment distributionsplotSegmentDistribution
Simulate markers conditional on a given IBD patternprofileSimIBD
Realised relatednessrealised realisedIdentity realisedInbreeding realisedKappa realisedKinship
Summary statistics for identified segmentssegmentStats
Uniform recombination mapsuniformMap
Probability of zero IBDzeroIBD