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

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Documentation for package ‘hapFabia’ version 1.34.0

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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