hapFabia

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

Bioconductor version: Release (2.14)

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

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("hapFabia")

To cite this package in a publication, start R and enter:

    citation("hapFabia")

Documentation

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

Details

biocViews Clustering, GeneticVariability, Genetics, Homo_sapiens, SNP, SequenceMatching, Sequencing, Software, Visualization
Version 1.6.0
In Bioconductor since BioC 2.11 (R-2.15)
License LGPL (>= 2.1)
Depends R (>= 2.12.0), Biobase, fabia(>= 2.3.1)
Imports methods, graphics, grDevices, stats, utils, KernSmooth
Suggests
System Requirements
URL http://www.bioinf.jku.at/software/hapFabia/hapFabia.html
Depends On Me
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Package Downloads

Package Source hapFabia_1.6.0.tar.gz
Windows Binary hapFabia_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) hapFabia_1.6.0.tgz
Mac OS X 10.9 (Mavericks)
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