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 |