Package: ibdsim2 2.3.3

Magnus Dehli Vigeland

ibdsim2: Simulation of Chromosomal Regions Shared by Family Members

Simulation of chromosomal segments shared identical-by-descent (IBD) among 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_2.3.3.tar.gz
ibdsim2_2.3.3.zip(r-4.7-x86_64)ibdsim2_2.3.3.zip(r-4.7-arm64)ibdsim2_2.3.3.zip(r-4.6-x86_64)ibdsim2_2.3.3.zip(r-4.6-arm64)ibdsim2_2.3.3.zip(r-4.5-x86_64)
ibdsim2_2.3.3.tgz(r-4.6-x86_64)ibdsim2_2.3.3.tgz(r-4.6-arm64)ibdsim2_2.3.3.tgz(r-4.5-x86_64)ibdsim2_2.3.3.tgz(r-4.5-arm64)
ibdsim2_2.3.3.tar.gz(r-4.7-arm64)ibdsim2_2.3.3.tar.gz(r-4.7-x86_64)ibdsim2_2.3.3.tar.gz(r-4.6-arm64)ibdsim2_2.3.3.tar.gz(r-4.6-x86_64)
ibdsim2_2.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ibdsim2/json (API)

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

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

Pkgdown/docs site:https://magnusdv.github.io

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

On CRAN:

Conda:

identity-by-descentrelatednesssimulationcpp

5.50 score 7 stars 2 packages 30 scripts 662 downloads 28 exports 32 dependencies

Last updated from:86c3f7be04. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK159
linux-devel-x86_64OK156
source / vignettesOK179
linux-release-arm64OK157
linux-release-x86_64OK151
macos-release-arm64OK145
macos-release-x86_64OK277
macos-oldrel-arm64OK124
macos-oldrel-x86_64OK216
windows-devel-arm64OK353
windows-devel-x86_64OK197
windows-release-arm64OK279
windows-release-x86_64OK115
windows-oldrel-x86_64OK145
wasm-releaseOK126

Exports:convertPoscustomMapestimateIdentityestimateInbreedingestimateKappaestimateKinshipestimateTwoLocusIdentityestimateTwoLocusInbreedingestimateTwoLocusKappaestimateTwoLocusKinshipextractIdsfindPatternhaploDrawibdsimkaryoHaploidlaunchApploadMapmapLenphysRangeplotSegmentDistributionprofileSimIBDrealisedIdentityrealisedInbreedingrealisedKapparealisedKinshipsegmentStatsuniformMapzeroIBD

Dependencies:clicpp11evaluatefarverggplot2gluegtablehighrisobandkinship2knitrlabelinglatticelifecyclelpSolveMatrixpedmutpedtoolsquadprogR6RColorBrewerRcppribdrlangS7scalesslamvctrsviridisLitewithrxfunyaml

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
Legacy version of the 'decode19' maplegacy_decode19
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