hapFabia
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
Bioconductor version: 3.23 · Package version: 1.54.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("hapFabia")Details
| Maintainer | Andreas Mitterecker <mitterecker@bioinf.jku.at> |
| Author | Sepp Hochreiter <hochreit@bioinf.jku.at> |
| License | LGPL (>= 2.1) |
| URL | http://www.bioinf.jku.at/software/hapFabia/hapFabia.html |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, GeneticVariability, Genetics, SNP, SequenceMatching, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/hapFabia/ |
Citation
From within R, enter citation("hapFabia"):
Sepp Hochreiter. hapFabia: hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data. doi:10.18129/B9.bioc.hapFabia, R package version 1.54.0, https://bioconductor.org/packages/hapFabia.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | hapFabia_1.54.0.tar.gz |
| Windows binary (x86_64) | hapFabia_1.54.0.zip |
| macOS binary (arm64) | hapFabia_1.54.0.tgz |
| macOS binary (x86_64) | hapFabia_1.54.0.tgz |
Dependencies
Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1)
Imports: methods, graphics, grDevices, stats, utils