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 |