Package: hapFabia
Title: hapFabia: Identification of very short segments of identity by
        descent (IBD) characterized by rare variants in large
        sequencing data
Version: 1.40.0
Date: 2017-03-11
Author: Sepp Hochreiter <hochreit@bioinf.jku.at>
Maintainer: Andreas Mitterecker <mitterecker@bioinf.jku.at>
Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1)
Imports: methods, graphics, grDevices, stats, utils
LinkingTo:
Description: 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.
License: LGPL (>= 2.1)
Collate: AllClasses.R AllGenerics.R hapFabia.R
        methods-Factorization-class.R methods-IBDsegment-class.R
        methods-IBDsegmentList-class.R zzz.R
URL: http://www.bioinf.jku.at/software/hapFabia/hapFabia.html
biocViews: Genetics, GeneticVariability, SNP, Sequencing, Sequencing,
        Visualization, Clustering, SequenceMatching, Software
git_url: https://git.bioconductor.org/packages/hapFabia
git_branch: RELEASE_3_16
git_last_commit: 4ccfc31
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
NeedsCompilation: yes
Packaged: 2022-11-01 21:44:35 UTC; biocbuild
Built: R 4.2.3; x86_64-conda-linux-gnu; 2023-05-18 22:57:25 UTC; unix
