A B C E F H I L M N P R S T V misc
| analyzeHaploClusters | Loop over extracted haplotype clusters to supply a descriptive statistics |
| 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 |
| 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 |
| extractHaploClusters | Extract haplotype clusters from a 'fabia' result |
| extractHaploClusters-method | Extract haplotype clusters from a 'fabia' result |
| findDenseRegions | Find accumulations of values via histogram counts |
| 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' |
| 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' |
| 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 |
| 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 |
| 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 |
| 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 |
| res | Example result of 'spfabia' |
| 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 |
| 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' |
| vcftoFABIA | Converting genotyping data from 'vcf' to sparse matrix format |
| [ | 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 |