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

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.

AuthorSepp Hochreiter <hochreit@bioinf.jku.at>
Date of publicationNone
MaintainerSepp Hochreiter <hochreit@bioinf.jku.at>
LicenseLGPL (>= 2.1)
Version1.16.0
http://www.bioinf.jku.at/software/hapFabia/hapFabia.html

View on Bioconductor

Man pages

analyzeIBDsegments: Loop over extracted IBD segments to supply a descriptive...

chr1ASW1000G: Example genotype data in 'vcf' format

compareIBDsegmentLists: Hierarchical clustering of IBD segments stored in IBD segment...

extractIBDsegments: Extract IBD segments from a 'fabia' result

findDenseRegions: Find accumulations of values via histogram counts

hapFabia: IBD segment extraction by FABIA

hapFabiaVersion: Display version info for package 'hapFabia'

hapRes: Example result of 'hapFabia'

IBDsegment-class: IBDsegment instances and methods

IBDsegmentList2excel: Store an IBD segment list in EXCEL / csv format

IBDsegmentList-class: IBDsegmentList instances and methods

identifyDuplicates: Identify duplicates of IBD segments

iterateIntervals: Loop over DNA intervals with a call of 'hapFabia'

makePipelineFile: Generate 'pipleline.R'

matrixPlot: Basic plot function for IBD segments

mergedIBDsegmentList: Example IBD segment list as a result of 'hapFabia'

mergeIBDsegmentLists: Merging IBD segments

plotIBDsegment: Plots an IBD segment given genotype data and tagSNVs

res: Example result of 'spfabia'

setAnnotation: Fills in annotations of tagSNVs of a list of IBD segments

setStatistics: Computes and stores the statistics of an IBD segment list

sim: Similarity measures for IBD segments

simu: Example simulation data for 'hapFabia'

simulateIBDsegments: Generates simulated genotyping data with IBD segments

simulateIBDsegmentsFabia: Generates simulated genotyping data with IBD segments for...

split_sparse_matrix: Splits genotyping data in sparse matrix format into intervals

toolsFactorizationClass: Tools to analyze results of 'fabia'

vcftoFABIA: Converting genotyping data from 'vcf' to sparse matrix format

Files in this package

hapFabia/DESCRIPTION
hapFabia/NAMESPACE
hapFabia/NEWS
hapFabia/R
hapFabia/R/AllClasses.R hapFabia/R/AllGenerics.R hapFabia/R/hapFabia.R hapFabia/R/methods-Factorization-class.R hapFabia/R/methods-IBDsegment-class.R hapFabia/R/methods-IBDsegmentList-class.R hapFabia/R/zzz.R
hapFabia/build
hapFabia/build/vignette.rds
hapFabia/cleanup
hapFabia/data
hapFabia/data/chr1ASW1000G.RData
hapFabia/data/hapRes.RData
hapFabia/data/mergedIBDsegmentList.RData
hapFabia/data/res.RData
hapFabia/data/simu.RData
hapFabia/inst
hapFabia/inst/CITATION
hapFabia/inst/doc
hapFabia/inst/doc/hapfabia.R
hapFabia/inst/doc/hapfabia.Rnw
hapFabia/inst/doc/hapfabia.pdf
hapFabia/inst/pipeline
hapFabia/inst/pipeline/pipeline.R
hapFabia/man
hapFabia/man/IBDsegment-class.Rd hapFabia/man/IBDsegmentList-class.Rd hapFabia/man/IBDsegmentList2excel.Rd hapFabia/man/analyzeIBDsegments.Rd hapFabia/man/chr1ASW1000G.Rd hapFabia/man/compareIBDsegmentLists.Rd hapFabia/man/extractIBDsegments.Rd hapFabia/man/findDenseRegions.Rd hapFabia/man/hapFabia.Rd hapFabia/man/hapFabiaVersion.Rd hapFabia/man/hapRes.Rd hapFabia/man/identifyDuplicates.Rd hapFabia/man/iterateIntervals.Rd hapFabia/man/makePipelineFile.Rd hapFabia/man/matrixPlot.Rd hapFabia/man/mergeIBDsegmentLists.Rd hapFabia/man/mergedIBDsegmentList.Rd hapFabia/man/plotIBDsegment.Rd hapFabia/man/res.Rd hapFabia/man/setAnnotation.Rd hapFabia/man/setStatistics.Rd hapFabia/man/sim.Rd hapFabia/man/simu.Rd hapFabia/man/simulateIBDsegments.Rd hapFabia/man/simulateIBDsegmentsFabia.Rd hapFabia/man/split_sparse_matrix.Rd hapFabia/man/toolsFactorizationClass.Rd hapFabia/man/vcftoFABIA.Rd
hapFabia/src
hapFabia/src/Makevars
hapFabia/src/Makevars.win
hapFabia/src/commandLine
hapFabia/src/commandLine/split_sparse_matrix.c
hapFabia/src/commandLine/vcftoFABIA.c
hapFabia/src/interfaceR.c
hapFabia/src/split_sparse_matrixB.c
hapFabia/src/vcftoFABIAB.c
hapFabia/vignettes
hapFabia/vignettes/bioinf-article.txi
hapFabia/vignettes/bioinf-bar.png
hapFabia/vignettes/bioinf.cls
hapFabia/vignettes/figures
hapFabia/vignettes/figures/example1.pdf
hapFabia/vignettes/figures/example8.pdf
hapFabia/vignettes/figures/pedi.pdf
hapFabia/vignettes/figures/plotB1.pdf
hapFabia/vignettes/figures/vectors_new.pdf
hapFabia/vignettes/hapfabia.Rnw
hapFabia/vignettes/ibd.bib
hapFabia/vignettes/natbib.bst
hapFabia/vignettes/natbib.sty

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