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

## Documentation for package ‘hapFabia’ version 1.16.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C E F H I L M N P R S T V misc

## -- A --

analyzeIBDsegments | Loop over extracted IBD segments to supply a descriptive statistics

## -- B --

bicluster_id | IBDsegment instances and methods
bicluster_id-method | IBDsegment instances and methods
bicluster_id<- | IBDsegment instances and methods
bicluster_id<--method | IBDsegment instances and methods

## -- C --

chr1ASW1000G | Example genotype data in 'vcf' format
chromosome | IBDsegment instances and methods
chromosome-method | IBDsegment instances and methods
chromosome<- | IBDsegment instances and methods
chromosome<--method | IBDsegment instances and methods
compareIBDsegmentLists | Hierarchical clustering of IBD segments stored in IBD segment list(s)
compareIBDsegmentLists-method | Hierarchical clustering of IBD segments stored in IBD segment list(s)
coreClusterIndividuals | IBDsegment instances and methods
coreClusterIndividuals-method | IBDsegment instances and methods
coreClusterIndividuals<- | IBDsegment instances and methods
coreClusterIndividuals<--method | IBDsegment instances and methods

## -- E --

extractIBDsegments | Extract IBD segments from a 'fabia' result
extractIBDsegments-method | Extract IBD segments from a 'fabia' result

## -- F --

findDenseRegions | Find accumulations of values via histogram counts

## -- H --

hapFabia | IBD segment extraction by FABIA
hapFabiaVersion | Display version info for package 'hapFabia'
hapRes | Example result of 'hapFabia'
histL | Tools to analyze results of 'fabia'
histL-method | Tools to analyze results of 'fabia'

## -- I --

IBDsegment | IBDsegment instances and methods
IBDsegment-class | IBDsegment instances and methods
IBDsegment-method | IBDsegment instances and methods
IBDsegmentLength | IBDsegment instances and methods
IBDsegmentLength-method | IBDsegment instances and methods
IBDsegmentLength<- | IBDsegment instances and methods
IBDsegmentLength<--method | IBDsegment instances and methods
IBDsegmentList | IBDsegmentList instances and methods
IBDsegmentList-class | IBDsegmentList instances and methods
IBDsegmentList-method | IBDsegmentList instances and methods
IBDsegmentList2excel | Store an IBD segment list in EXCEL / csv format
IBDsegmentList2excel-method | Store an IBD segment list in EXCEL / csv format
IBDsegmentPos | IBDsegment instances and methods
IBDsegmentPos-method | IBDsegment instances and methods
IBDsegmentPos<- | IBDsegment instances and methods
IBDsegmentPos<--method | IBDsegment instances and methods
IBDsegments | IBDsegmentList instances and methods
IBDsegments-method | IBDsegmentList instances and methods
IBDsegments<- | IBDsegmentList instances and methods
IBDsegments<--method | IBDsegmentList instances and methods
ID | IBDsegment instances and methods
ID-method | IBDsegment instances and methods
ID<- | IBDsegment instances and methods
ID<--method | IBDsegment instances and methods
identifyDuplicates | Identify duplicates of IBD segments
idIndividuals | IBDsegment instances and methods
idIndividuals-method | IBDsegment instances and methods
idIndividuals<- | IBDsegment instances and methods
idIndividuals<--method | IBDsegment instances and methods
individualPerTagSNV | IBDsegment instances and methods
individualPerTagSNV-method | IBDsegment instances and methods
individualPerTagSNV<- | IBDsegment instances and methods
individualPerTagSNV<--method | IBDsegment instances and methods
individuals | IBDsegment instances and methods
individuals-method | IBDsegment instances and methods
individuals<- | IBDsegment instances and methods
individuals<--method | IBDsegment instances and methods
iterateIntervals | Loop over DNA intervals with a call of 'hapFabia'

## -- L --

labelIndividuals | IBDsegment instances and methods
labelIndividuals-method | IBDsegment instances and methods
labelIndividuals<- | IBDsegment instances and methods
labelIndividuals<--method | IBDsegment instances and methods
lengthList | IBDsegmentList instances and methods
lengthList-method | IBDsegmentList instances and methods
lengthList<- | IBDsegmentList instances and methods
lengthList<--method | IBDsegmentList instances and methods

## -- M --

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
mergeIBDsegmentLists-method | Merging IBD segments

## -- N --

numberIndividuals | IBDsegment instances and methods
numberIndividuals-method | IBDsegment instances and methods
numberIndividuals<- | IBDsegment instances and methods
numberIndividuals<--method | IBDsegment instances and methods
numbertagSNVs | IBDsegment instances and methods
numbertagSNVs-method | IBDsegment instances and methods
numbertagSNVs<- | IBDsegment instances and methods
numbertagSNVs<--method | IBDsegment instances and methods

## -- P --

platformIndividuals | IBDsegment instances and methods
platformIndividuals-method | IBDsegment instances and methods
platformIndividuals<- | IBDsegment instances and methods
platformIndividuals<--method | IBDsegment instances and methods
plot-method | IBDsegment instances and methods
plot-method | IBDsegmentList instances and methods
plotIBDsegment | Plots an IBD segment given genotype data and tagSNVs
plotL | Tools to analyze results of 'fabia'
plotL-method | Tools to analyze results of 'fabia'
plotLarger | IBDsegment instances and methods
plotLarger-method | IBDsegment instances and methods
populationIndividuals | IBDsegment instances and methods
populationIndividuals-method | IBDsegment instances and methods
populationIndividuals<- | IBDsegment instances and methods
populationIndividuals<--method | IBDsegment instances and methods

## -- R --

res | Example result of 'spfabia'

## -- S --

setAnnotation | Fills in annotations of tagSNVs of a list of IBD segments
setAnnotation-method | Fills in annotations of tagSNVs of a list of IBD segments
setStatistics | Computes and stores the statistics of an IBD segment list
setStatistics-method | 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 'fabia'
split_sparse_matrix | Splits genotyping data in sparse matrix format into intervals
statistics | IBDsegmentList instances and methods
statistics-method | IBDsegmentList instances and methods
statistics<- | IBDsegmentList instances and methods
statistics<--method | IBDsegmentList instances and methods
summary-method | IBDsegment instances and methods
summary-method | IBDsegmentList instances and methods

## -- T --

tagSNVAlleles | IBDsegment instances and methods
tagSNVAlleles-method | IBDsegment instances and methods
tagSNVAlleles<- | IBDsegment instances and methods
tagSNVAlleles<--method | IBDsegment instances and methods
tagSNVAnno | IBDsegment instances and methods
tagSNVAnno-method | IBDsegment instances and methods
tagSNVAnno<- | IBDsegment instances and methods
tagSNVAnno<--method | IBDsegment instances and methods
tagSNVChange | IBDsegment instances and methods
tagSNVChange-method | IBDsegment instances and methods
tagSNVChange<- | IBDsegment instances and methods
tagSNVChange<--method | IBDsegment instances and methods
tagSNVFreq | IBDsegment instances and methods
tagSNVFreq-method | IBDsegment instances and methods
tagSNVFreq<- | IBDsegment instances and methods
tagSNVFreq<--method | IBDsegment instances and methods
tagSNVGroupFreq | IBDsegment instances and methods
tagSNVGroupFreq-method | IBDsegment instances and methods
tagSNVGroupFreq<- | IBDsegment instances and methods
tagSNVGroupFreq<--method | IBDsegment instances and methods
tagSNVNames | IBDsegment instances and methods
tagSNVNames-method | IBDsegment instances and methods
tagSNVNames<- | IBDsegment instances and methods
tagSNVNames<--method | IBDsegment instances and methods
tagSNVPositions | IBDsegment instances and methods
tagSNVPositions-method | IBDsegment instances and methods
tagSNVPositions<- | IBDsegment instances and methods
tagSNVPositions<--method | IBDsegment instances and methods
tagSNVs | IBDsegment instances and methods
tagSNVs-method | IBDsegment instances and methods
tagSNVs<- | IBDsegment instances and methods
tagSNVs<--method | IBDsegment instances and methods
tagSNVsPerIndividual | IBDsegment instances and methods
tagSNVsPerIndividual-method | IBDsegment instances and methods
tagSNVsPerIndividual<- | IBDsegment instances and methods
tagSNVsPerIndividual<--method | IBDsegment instances and methods
toolsFactorizationClass | Tools to analyze results of 'fabia'
topLZ | Tools to analyze results of 'fabia'
topLZ-method | Tools to analyze results of 'fabia'

## -- V --

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

## -- misc --

[ | IBDsegmentList instances and methods
[-method | IBDsegmentList instances and methods
[<- | IBDsegmentList instances and methods
[<--method | IBDsegmentList instances and methods
[[ | IBDsegmentList instances and methods
[[-method | IBDsegmentList instances and methods
[[<- | IBDsegmentList instances and methods
[[<--method | IBDsegmentList instances and methods