# hapFabia: Identification of rare and short haplotype clusters in large sequencing data

## Documentation for package ‘hapFabia’ version 1.0.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

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

## -- A --

analyzeHaploClusters | Loop over extracted haplotype clusters to supply a descriptive statistics

## -- B --

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

## -- C --

chr1ASW1000G | Example genotype data in 'vcf' format
chromosome | HaploCluster instances and methods
chromosome-method | HaploCluster instances and methods
chromosome<- | HaploCluster instances and methods
chromosome<--method | HaploCluster instances and methods
compareHaploClusterLists | Hierarchical clustering of haplotype clusters stored in haplotype cluster list(s)
compareHaploClusterLists-method | Hierarchical clustering of haplotype clusters stored in haplotype cluster list(s)
coreClusterIndividuals | HaploCluster instances and methods
coreClusterIndividuals-method | HaploCluster instances and methods
coreClusterIndividuals<- | HaploCluster instances and methods
coreClusterIndividuals<--method | HaploCluster instances and methods

## -- E --

extractHaploClusters | Extract haplotype clusters from a 'fabia' result
extractHaploClusters-method | Extract haplotype clusters from a 'fabia' result

## -- F --

findDenseRegions | Find accumulations of values via histogram counts

## -- H --

hapFabia | Haplotype cluster extraction by FABIA
hapFabiaVersion | Display version info for package 'hapFabia'
HaploCluster | HaploCluster instances and methods
HaploCluster-class | HaploCluster instances and methods
HaploCluster-method | HaploCluster instances and methods
haploClusterLength | HaploCluster instances and methods
haploClusterLength-method | HaploCluster instances and methods
haploClusterLength<- | HaploCluster instances and methods
haploClusterLength<--method | HaploCluster instances and methods
HaploClusterList | HaploClusterList instances and methods
HaploClusterList-class | HaploClusterList instances and methods
HaploClusterList-method | HaploClusterList instances and methods
haploClusterList2excel | Store a haplotype cluster list in EXCEL / csv format
haploClusterList2excel-method | Store a haplotype cluster list in EXCEL / csv format
haploClusterPos | HaploCluster instances and methods
haploClusterPos-method | HaploCluster instances and methods
haploClusterPos<- | HaploCluster instances and methods
haploClusterPos<--method | HaploCluster instances and methods
haploClusters | HaploClusterList instances and methods
haploClusters-method | HaploClusterList instances and methods
haploClusters<- | HaploClusterList instances and methods
haploClusters<--method | HaploClusterList instances and methods
hapRes | Example result of 'hapFabia'
histL | Tools to analyze results of 'fabia'
histL-method | Tools to analyze results of 'fabia'

## -- I --

ID | HaploCluster instances and methods
ID-method | HaploCluster instances and methods
ID<- | HaploCluster instances and methods
ID<--method | HaploCluster instances and methods
identifyDuplicates | Identify duplicates of haplotype clusters
idIndividuals | HaploCluster instances and methods
idIndividuals-method | HaploCluster instances and methods
idIndividuals<- | HaploCluster instances and methods
idIndividuals<--method | HaploCluster instances and methods
individualPerTagSNV | HaploCluster instances and methods
individualPerTagSNV-method | HaploCluster instances and methods
individualPerTagSNV<- | HaploCluster instances and methods
individualPerTagSNV<--method | HaploCluster instances and methods
individuals | HaploCluster instances and methods
individuals-method | HaploCluster instances and methods
individuals<- | HaploCluster instances and methods
individuals<--method | HaploCluster instances and methods
iterateSegments | Loop over DNA segments with a call of 'hapFabia'

## -- L --

labelIndividuals | HaploCluster instances and methods
labelIndividuals-method | HaploCluster instances and methods
labelIndividuals<- | HaploCluster instances and methods
labelIndividuals<--method | HaploCluster instances and methods
lengthList | HaploClusterList instances and methods
lengthList-method | HaploClusterList instances and methods
lengthList<- | HaploClusterList instances and methods
lengthList<--method | HaploClusterList instances and methods

## -- M --

makePipelineFile | Generate 'pipleline.R'
matrixPlot | Basic plot function for haplotype clusters
mergedHaploClusterList | Example haplotype cluster list as a result of 'hapFabia'
mergeHaploClusterLists | Merging haplotype clusters
mergeHaploClusterLists-method | Merging haplotype clusters

## -- N --

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

## -- P --

platformIndividuals | HaploCluster instances and methods
platformIndividuals-method | HaploCluster instances and methods
platformIndividuals<- | HaploCluster instances and methods
platformIndividuals<--method | HaploCluster instances and methods
plot-method | HaploCluster instances and methods
plot-method | HaploClusterList instances and methods
plotHaplotypeCluster | Plots a haplotype cluster given genotype data and tagSNVs
plotL | Tools to analyze results of 'fabia'
plotL-method | Tools to analyze results of 'fabia'
populationIndividuals | HaploCluster instances and methods
populationIndividuals-method | HaploCluster instances and methods
populationIndividuals<- | HaploCluster instances and methods
populationIndividuals<--method | HaploCluster instances and methods

## -- R --

res | Example result of 'spfabia'

## -- S --

setAnnotation | Fills in annotations of tagSNVs of a list of haplotype clusters
setAnnotation-method | Fills in annotations of tagSNVs of a list of haplotype clusters
setStatistics | Computes and stores the statistics of a haplotype cluster list
setStatistics-method | Computes and stores the statistics of a haplotype cluster list
sim | Similarity measures for haplotype clusters
simu | Example simulation data for 'hapFabia'
simulateHaploClustersFabia | Generates simulated genotyping data with haplotype clusters for 'fabia'
simulateHaplotypeClusters | Generates simulated genotyping data with haplotype clusters
split_sparse_matrix | Splits genotyping data in sparse matrix format into segments
statistics | HaploClusterList instances and methods
statistics-method | HaploClusterList instances and methods
statistics<- | HaploClusterList instances and methods
statistics<--method | HaploClusterList instances and methods
summary-method | HaploCluster instances and methods
summary-method | HaploClusterList instances and methods

## -- T --

tagSNVAlleles | HaploCluster instances and methods
tagSNVAlleles-method | HaploCluster instances and methods
tagSNVAlleles<- | HaploCluster instances and methods
tagSNVAlleles<--method | HaploCluster instances and methods
tagSNVAnno | HaploCluster instances and methods
tagSNVAnno-method | HaploCluster instances and methods
tagSNVAnno<- | HaploCluster instances and methods
tagSNVAnno<--method | HaploCluster instances and methods
tagSNVChange | HaploCluster instances and methods
tagSNVChange-method | HaploCluster instances and methods
tagSNVChange<- | HaploCluster instances and methods
tagSNVChange<--method | HaploCluster instances and methods
tagSNVFreq | HaploCluster instances and methods
tagSNVFreq-method | HaploCluster instances and methods
tagSNVFreq<- | HaploCluster instances and methods
tagSNVFreq<--method | HaploCluster instances and methods
tagSNVGroupFreq | HaploCluster instances and methods
tagSNVGroupFreq-method | HaploCluster instances and methods
tagSNVGroupFreq<- | HaploCluster instances and methods
tagSNVGroupFreq<--method | HaploCluster instances and methods
tagSNVNames | HaploCluster instances and methods
tagSNVNames-method | HaploCluster instances and methods
tagSNVNames<- | HaploCluster instances and methods
tagSNVNames<--method | HaploCluster instances and methods
tagSNVPositions | HaploCluster instances and methods
tagSNVPositions-method | HaploCluster instances and methods
tagSNVPositions<- | HaploCluster instances and methods
tagSNVPositions<--method | HaploCluster instances and methods
tagSNVs | HaploCluster instances and methods
tagSNVs-method | HaploCluster instances and methods
tagSNVs<- | HaploCluster instances and methods
tagSNVs<--method | HaploCluster instances and methods
tagSNVsPerIndividual | HaploCluster instances and methods
tagSNVsPerIndividual-method | HaploCluster instances and methods
tagSNVsPerIndividual<- | HaploCluster instances and methods
tagSNVsPerIndividual<--method | HaploCluster 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 --

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