A B C E F H I L M N P R S T V misc
analyzeIBDsegments | Loop over extracted IBD segments to supply a descriptive statistics |
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 |
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 |
extractIBDsegments | Extract IBD segments from a 'fabia' result |
extractIBDsegments-method | 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' |
histL | Tools to analyze results of 'fabia' |
histL-method | Tools to analyze results of 'fabia' |
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' |
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 |
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 |
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 |
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 |
res | Example result of 'spfabia' |
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 |
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' |
vcftoFABIA | Converting genotyping data from 'vcf' to sparse matrix format |
[ | 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 |