hapFabia

DOI: 10.18129/B9.bioc.hapFabia  

hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

Bioconductor version: Release (3.16)

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.

Author: Sepp Hochreiter <hochreit at bioinf.jku.at>

Maintainer: Andreas Mitterecker <mitterecker at bioinf.jku.at>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("hapFabia")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("hapFabia")

 

PDF	R Script	hapFabia: Manual for the R package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, GeneticVariability, Genetics, SNP, SequenceMatching, Sequencing, Software, Visualization
Version	1.40.0
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 years)
License	LGPL (>= 2.1)
Depends	R (>= 3.6.0), Biobase, fabia(>= 2.3.1)
Imports	methods, graphics, grDevices, stats, utils
LinkingTo
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SystemRequirements
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URL	http://www.bioinf.jku.at/software/hapFabia/hapFabia.html
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	hapFabia_1.40.0.tar.gz
Windows Binary	hapFabia_1.40.0.zip (64-bit only)
macOS Binary (x86_64)	hapFabia_1.40.0.tgz
macOS Binary (arm64)	hapFabia_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/hapFabia
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/hapFabia
Bioc Package Browser	https://code.bioconductor.org/browse/hapFabia/
Package Short Url	https://bioconductor.org/packages/hapFabia/
Package Downloads Report	Download Stats