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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("hapFabia")
AuthorSepp Hochreiter <hochreit@bioinf.jku.at>
Bioconductor views Clustering GeneticVariability Genetics SNP SequenceMatching Sequencing Software Visualization
Date of publicationNone
MaintainerSepp Hochreiter <hochreit@bioinf.jku.at>
LicenseLGPL (>= 2.1)
Version1.18.0
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

Functions

[ Man page
[<- Man page
[[ Man page
[[<- Man page
analyzeIBDsegments Man page
bicluster_id Man page
bicluster_id<- Man page
bicluster_id,IBDsegment-method Man page
bicluster_id<-,IBDsegment,numeric-method Man page
chr1ASW1000G Man page
chromosome Man page
chromosome<- Man page
chromosome<-,IBDsegment,character-method Man page
chromosome,IBDsegment-method Man page
compareIBDsegmentLists Man page
compareIBDsegmentLists,IBDsegmentList,ANY,character,ANY,ANY,nume Man page
compareIBDsegmentLists,IBDsegmentList-method Man page
coreClusterIndividuals Man page
coreClusterIndividuals<- Man page
coreClusterIndividuals,IBDsegment-method Man page
coreClusterIndividuals<-,IBDsegment,vector-method Man page
extractIBDsegments Man page
extractIBDsegments,Factorization,list,data.frame,character,matri Man page
extractIBDsegments,Factorization-method Man page
findDenseRegions Man page
hapFabia Man page
hapFabiaVersion Man page
hapRes Man page
histL Man page
histL,Factorization-method Man page
histL,Factorization,numeric,ANY,ANY,numeric,numeric-method Man page
IBDsegment Man page
IBDsegment,ANY-method Man page
IBDsegment-class Man page
IBDsegment,IBDsegment-method Man page
IBDsegmentLength Man page
IBDsegmentLength<- Man page
IBDsegmentLength,IBDsegment-method Man page
IBDsegmentLength<-,IBDsegment,numeric-method Man page
IBDsegmentList Man page
IBDsegmentList2excel Man page
IBDsegmentList2excel,IBDsegmentList,character-method Man page
IBDsegmentList2excel,IBDsegmentList-method Man page
IBDsegmentList,ANY-method Man page
IBDsegmentList-class Man page
IBDsegmentList,list,numeric,list-method Man page
[<-,IBDsegmentList-method Man page
[,IBDsegmentList-method Man page
[[<-,IBDsegmentList-method Man page
[[,IBDsegmentList-method Man page
IBDsegmentList-method Man page
[<-,IBDsegmentList,numeric,missing,IBDsegmentList-method Man page
[[<-,IBDsegmentList,numeric,missing,IBDsegment-method Man page
[,IBDsegmentList,numeric,missing-method Man page
[[,IBDsegmentList,numeric,missing-method Man page
IBDsegment-method Man page
IBDsegment,numeric,numeric,character,numeric,numeric,numeric,num Man page
IBDsegmentPos Man page
IBDsegmentPos<- Man page
IBDsegmentPos,IBDsegment-method Man page
IBDsegmentPos<-,IBDsegment,numeric-method Man page
IBDsegments Man page
IBDsegments<- Man page
IBDsegments<-,IBDsegmentList,list-method Man page
IBDsegments,IBDsegmentList-method Man page
ID Man page
ID<- Man page
identifyDuplicates Man page
ID,IBDsegment-method Man page
ID<-,IBDsegment,numeric-method Man page
idIndividuals Man page
idIndividuals<- Man page
idIndividuals,IBDsegment-method Man page
idIndividuals<-,IBDsegment,vector-method Man page
individualPerTagSNV Man page
individualPerTagSNV<- Man page
individualPerTagSNV,IBDsegment-method Man page
individualPerTagSNV<-,IBDsegment,vector-method Man page
individuals Man page
individuals<- Man page
individuals,IBDsegment-method Man page
individuals<-,IBDsegment,vector-method Man page
iterateIntervals Man page
labelIndividuals Man page
labelIndividuals<- Man page
labelIndividuals,IBDsegment-method Man page
labelIndividuals<-,IBDsegment,vector-method Man page
lengthList Man page
lengthList<- Man page
lengthList,IBDsegmentList-method Man page
lengthList<-,IBDsegmentList,numeric-method Man page
makePipelineFile Man page
matrixPlot Man page
mergedIBDsegmentList Man page
mergeIBDsegmentLists Man page
mergeIBDsegmentLists,IBDsegmentList,ANY,vector-method Man page
mergeIBDsegmentLists,IBDsegmentList-method Man page
numberIndividuals Man page
numberIndividuals<- Man page
numberIndividuals,IBDsegment-method Man page
numberIndividuals<-,IBDsegment,numeric-method Man page
numbertagSNVs Man page
numbertagSNVs<- Man page
numbertagSNVs,IBDsegment-method Man page
numbertagSNVs<-,IBDsegment,numeric-method Man page
platformIndividuals Man page
platformIndividuals<- Man page
platformIndividuals,IBDsegment-method Man page
platformIndividuals<-,IBDsegment,vector-method Man page
plotIBDsegment Man page
plot,IBDsegmentList-method Man page
plot,IBDsegmentList,missing-method Man page
plot,IBDsegment-method Man page
plot,IBDsegment,missing-method Man page
plotL Man page
plotLarger Man page
plotLarger,IBDsegment,character,numeric-method Man page
plotLarger,IBDsegment-method Man page
plotLarger,IBDsegment,missing-method Man page
plotL,Factorization-method Man page
plotL,Factorization,numeric,ANY,ANY,character,numeric,numeric,ch Man page
populationIndividuals Man page
populationIndividuals<- Man page
populationIndividuals,IBDsegment-method Man page
populationIndividuals<-,IBDsegment,vector-method Man page
res Man page
setAnnotation Man page
setAnnotation,IBDsegmentList,character-method Man page
setAnnotation,IBDsegmentList-method Man page
setStatistics Man page
setStatistics,IBDsegmentList-method Man page
sim Man page
simu Man page
simulateIBDsegments Man page
simulateIBDsegmentsFabia Man page
split_sparse_matrix Man page
statistics Man page
statistics<- Man page
statistics<-,IBDsegmentList,list-method Man page
statistics,IBDsegmentList-method Man page
summary,IBDsegmentList-method Man page
summary,IBDsegment-method Man page
tagSNVAlleles Man page
tagSNVAlleles<- Man page
tagSNVAlleles,IBDsegment-method Man page
tagSNVAlleles<-,IBDsegment,vector-method Man page
tagSNVAnno Man page
tagSNVAnno<- Man page
tagSNVAnno,IBDsegment-method Man page
tagSNVAnno<-,IBDsegment,vector-method Man page
tagSNVChange Man page
tagSNVChange<- Man page
tagSNVChange,IBDsegment-method Man page
tagSNVChange<-,IBDsegment,vector-method Man page
tagSNVFreq Man page
tagSNVFreq<- Man page
tagSNVFreq,IBDsegment-method Man page
tagSNVFreq<-,IBDsegment,vector-method Man page
tagSNVGroupFreq Man page
tagSNVGroupFreq<- Man page
tagSNVGroupFreq,IBDsegment-method Man page
tagSNVGroupFreq<-,IBDsegment,vector-method Man page
tagSNVNames Man page
tagSNVNames<- Man page
tagSNVNames,IBDsegment-method Man page
tagSNVNames<-,IBDsegment,vector-method Man page
tagSNVPositions Man page
tagSNVPositions<- Man page
tagSNVPositions,IBDsegment-method Man page
tagSNVPositions<-,IBDsegment,vector-method Man page
tagSNVs Man page
tagSNVs<- Man page
tagSNVs,IBDsegment-method Man page
tagSNVs<-,IBDsegment,vector-method Man page
tagSNVsPerIndividual Man page
tagSNVsPerIndividual<- Man page
tagSNVsPerIndividual,IBDsegment-method Man page
tagSNVsPerIndividual<-,IBDsegment,vector-method Man page
toolsFactorizationClass Man page
topLZ Man page
topLZ,Factorization-method Man page
topLZ,Factorization,numeric,character,logical,ANY,ANY-method Man page
topLZ,Factorization,numeric,character,logical,ANY-method Man page
topLZ,Factorization,numeric,character,logical-method Man page
vcftoFABIA Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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