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


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Documentation for package ‘hapFabia’ version 1.0.0

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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