Package: ibdfindr 0.3.1

Magnus Dehli Vigeland

ibdfindr: HMM Toolkit for Inferring IBD Segments from SNP Genotypes

Implements continuous-time hidden Markov models (HMMs) to infer identity-by-descent (IBD) segments shared by two individuals from their single-nucleotide polymorphism (SNP) genotypes. Provides posterior probabilities at each marker (forward-backward algorithm), prediction of IBD segments (Viterbi algorithm), and functions for visualising results. Supports both autosomal data and X-chromosomal data.

Authors:Magnus Dehli Vigeland [aut, cre]

ibdfindr_0.3.1.tar.gz
ibdfindr_0.3.1.zip(r-4.7)ibdfindr_0.3.1.zip(r-4.6)ibdfindr_0.3.1.zip(r-4.5)
ibdfindr_0.3.1.tgz(r-4.6-any)ibdfindr_0.3.1.tgz(r-4.5-any)
ibdfindr_0.3.1.tar.gz(r-4.7-any)ibdfindr_0.3.1.tar.gz(r-4.6-any)
ibdfindr_0.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ibdfindr/json (API)
NEWS

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

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

Datasets:
  • brothersX - Dataset with X-chromosomal SNP genotypes for two brothers
  • cousinsDemo - Dataset with autosomal SNP genotypes for two cousins

On CRAN:

Conda:

4.68 score 4 stars 1 packages 4 scripts 498 downloads 7 exports 37 dependencies

Last updated from:d4d52f8c01. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK161
source / vignettesOK184
linux-release-x86_64OK158
macos-release-arm64OK129
macos-oldrel-arm64OK114
windows-develOK125
windows-releaseOK120
windows-oldrelOK109
wasm-releaseOK111

Exports:computePRfindIBDfindSegmentsfitHMMibdPosteriorsplotIBDtotalLoglik

Dependencies:clicpp11evaluatefarverforrelggplot2gluegtablehighribdsim2isobandkinship2knitrlabelinglatticelifecyclelpSolveMatrixpbapplypedmutpedprobrpedtoolsquadprogR6RColorBrewerRcppribdrlangS7scalesslamvctrsverbalisrviridisLitewithrxfunyaml