Package: hapFabia 1.49.0
Andreas Mitterecker
hapFabia: hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.
Authors:
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hapFabia.pdf |hapFabia.html✨
hapFabia/json (API)
NEWS
| # Install 'hapFabia' in R: |
| install.packages('hapFabia', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- chr1ASW1000G - Example genotype data in 'vcf' format
- hapRes - Example result of 'hapFabia'
- mergedIBDsegmentList - Example IBD segment list as a result of 'hapFabia'
- res - Example result of 'spfabia'
- simu - Example simulation data for 'hapFabia'
On BioConductor:hapFabia-1.47.0(bioc 3.20)hapFabia-1.46.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneticsgeneticvariabilitysnpsequencingvisualizationclusteringsequencematchingsoftware
Last updated 26 days agofrom:469b36178f. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.5-linux-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-mac-aarch64 | WARNING | Oct 30 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 30 2024 |
| R-4.3-mac-aarch64 | WARNING | Oct 30 2024 |
Exports:analyzeIBDsegmentsbicluster_idbicluster_id<-chromosomechromosome<-compareIBDsegmentListscoreClusterIndividualscoreClusterIndividuals<-extractIBDsegmentsfindDenseRegionshapFabiahapFabiaVersionhistLIBDsegmentIBDsegmentLengthIBDsegmentLength<-IBDsegmentListIBDsegmentList2excelIBDsegmentPosIBDsegmentPos<-IBDsegmentsIBDsegments<-IDID<-identifyDuplicatesidIndividualsidIndividuals<-individualPerTagSNVindividualPerTagSNV<-individualsindividuals<-iterateIntervalslabelIndividualslabelIndividuals<-lengthListlengthList<-makePipelineFilematrixPlotmergeIBDsegmentListsnumberIndividualsnumberIndividuals<-numbertagSNVsnumbertagSNVs<-platformIndividualsplatformIndividuals<-plotplotIBDsegmentplotLplotLargerpopulationIndividualspopulationIndividuals<-setAnnotationsetStatisticssimsimulateIBDsegmentssimulateIBDsegmentsFabiasplit_sparse_matrixstatisticsstatistics<-summarytagSNVAllelestagSNVAlleles<-tagSNVAnnotagSNVAnno<-tagSNVChangetagSNVChange<-tagSNVFreqtagSNVFreq<-tagSNVGroupFreqtagSNVGroupFreq<-tagSNVNamestagSNVNames<-tagSNVPositionstagSNVPositions<-tagSNVstagSNVs<-tagSNVsPerIndividualtagSNVsPerIndividual<-topLZvcftoFABIA
Dependencies:BiobaseBiocGenericsfabia
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Loop over extracted IBD segments to supply a descriptive statistics | analyzeIBDsegments |
| Example genotype data in 'vcf' format | chr1ASW1000G |
| Hierarchical clustering of IBD segments stored in IBD segment list(s) | compareIBDsegmentLists compareIBDsegmentLists,IBDsegmentList,ANY,character,ANY,ANY,numeric,numeric-method compareIBDsegmentLists,IBDsegmentList-method |
| Extract IBD segments from a 'fabia' result | extractIBDsegments extractIBDsegments,Factorization,list,data.frame,character,matrix,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric-method extractIBDsegments,Factorization-method |
| Find accumulations of values via histogram counts | findDenseRegions |
| IBD segment extraction by FABIA | hapFabia |
| Display version info for package 'hapFabia' | hapFabiaVersion |
| Example result of 'hapFabia' | hapRes |
| IBDsegment instances and methods | bicluster_id bicluster_id,IBDsegment-method bicluster_id<- bicluster_id<-,IBDsegment,numeric-method chromosome chromosome,IBDsegment-method chromosome<- chromosome<-,IBDsegment,character-method coreClusterIndividuals coreClusterIndividuals,IBDsegment-method coreClusterIndividuals<- coreClusterIndividuals<-,IBDsegment,vector-method IBDsegment IBDsegment,ANY-method IBDsegment,IBDsegment-method IBDsegment,numeric,numeric,character,numeric,numeric,numeric,numeric,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector-method IBDsegment-class IBDsegment-method IBDsegmentLength IBDsegmentLength,IBDsegment-method IBDsegmentLength<- IBDsegmentLength<-,IBDsegment,numeric-method IBDsegmentPos IBDsegmentPos,IBDsegment-method IBDsegmentPos<- IBDsegmentPos<-,IBDsegment,numeric-method ID ID,IBDsegment-method ID<- ID<-,IBDsegment,numeric-method idIndividuals idIndividuals,IBDsegment-method idIndividuals<- idIndividuals<-,IBDsegment,vector-method individualPerTagSNV individualPerTagSNV,IBDsegment-method individualPerTagSNV<- individualPerTagSNV<-,IBDsegment,vector-method individuals individuals,IBDsegment-method individuals<- individuals<-,IBDsegment,vector-method labelIndividuals labelIndividuals,IBDsegment-method labelIndividuals<- labelIndividuals<-,IBDsegment,vector-method numberIndividuals numberIndividuals,IBDsegment-method numberIndividuals<- numberIndividuals<-,IBDsegment,numeric-method numbertagSNVs numbertagSNVs,IBDsegment-method numbertagSNVs<- numbertagSNVs<-,IBDsegment,numeric-method platformIndividuals platformIndividuals,IBDsegment-method platformIndividuals<- platformIndividuals<-,IBDsegment,vector-method plot,IBDsegment,missing-method plot,IBDsegment-method plotLarger plotLarger,IBDsegment,character,numeric-method plotLarger,IBDsegment,missing-method plotLarger,IBDsegment-method populationIndividuals populationIndividuals,IBDsegment-method populationIndividuals<- populationIndividuals<-,IBDsegment,vector-method summary,IBDsegment-method tagSNVAlleles tagSNVAlleles,IBDsegment-method tagSNVAlleles<- tagSNVAlleles<-,IBDsegment,vector-method tagSNVAnno tagSNVAnno,IBDsegment-method tagSNVAnno<- tagSNVAnno<-,IBDsegment,vector-method tagSNVChange tagSNVChange,IBDsegment-method tagSNVChange<- tagSNVChange<-,IBDsegment,vector-method tagSNVFreq tagSNVFreq,IBDsegment-method tagSNVFreq<- tagSNVFreq<-,IBDsegment,vector-method tagSNVGroupFreq tagSNVGroupFreq,IBDsegment-method tagSNVGroupFreq<- tagSNVGroupFreq<-,IBDsegment,vector-method tagSNVNames tagSNVNames,IBDsegment-method tagSNVNames<- tagSNVNames<-,IBDsegment,vector-method tagSNVPositions tagSNVPositions,IBDsegment-method tagSNVPositions<- tagSNVPositions<-,IBDsegment,vector-method tagSNVs tagSNVs,IBDsegment-method tagSNVs<- tagSNVs<-,IBDsegment,vector-method tagSNVsPerIndividual tagSNVsPerIndividual,IBDsegment-method tagSNVsPerIndividual<- tagSNVsPerIndividual<-,IBDsegment,vector-method |
| IBDsegmentList instances and methods | IBDsegmentList IBDsegmentList,ANY-method IBDsegmentList,list,numeric,list-method IBDsegmentList-class IBDsegmentList-method IBDsegments IBDsegments,IBDsegmentList-method IBDsegments<- IBDsegments<-,IBDsegmentList,list-method lengthList lengthList,IBDsegmentList-method lengthList<- lengthList<-,IBDsegmentList,numeric-method plot,IBDsegmentList,missing-method plot,IBDsegmentList-method statistics statistics,IBDsegmentList-method statistics<- statistics<-,IBDsegmentList,list-method summary,IBDsegmentList-method [ [,IBDsegmentList,numeric,missing-method [,IBDsegmentList-method [<- [<-,IBDsegmentList,numeric,missing,IBDsegmentList-method [<-,IBDsegmentList-method [[ [[,IBDsegmentList,numeric,missing-method [[,IBDsegmentList-method [[<- [[<-,IBDsegmentList,numeric,missing,IBDsegment-method [[<-,IBDsegmentList-method |
| Store an IBD segment list in EXCEL / csv format | IBDsegmentList2excel IBDsegmentList2excel,IBDsegmentList,character-method IBDsegmentList2excel,IBDsegmentList-method |
| Identify duplicates of IBD segments | identifyDuplicates |
| Loop over DNA intervals with a call of 'hapFabia' | iterateIntervals |
| Generate 'pipleline.R' | makePipelineFile |
| Basic plot function for IBD segments | matrixPlot |
| Example IBD segment list as a result of 'hapFabia' | mergedIBDsegmentList |
| Merging IBD segments | mergeIBDsegmentLists mergeIBDsegmentLists,IBDsegmentList,ANY,vector-method mergeIBDsegmentLists,IBDsegmentList-method |
| Plots an IBD segment given genotype data and tagSNVs | plotIBDsegment |
| Example result of 'spfabia' | res |
| Fills in annotations of tagSNVs of a list of IBD segments | setAnnotation setAnnotation,IBDsegmentList,character-method setAnnotation,IBDsegmentList-method |
| Computes and stores the statistics of an IBD segment list | setStatistics setStatistics,IBDsegmentList-method |
| Similarity measures for IBD segments | sim |
| Example simulation data for 'hapFabia' | simu |
| Generates simulated genotyping data with IBD segments | simulateIBDsegments |
| Generates simulated genotyping data with IBD segments for 'fabia' | simulateIBDsegmentsFabia |
| Splits genotyping data in sparse matrix format into intervals | split_sparse_matrix |
| Tools to analyze results of 'fabia' | histL histL,Factorization,numeric,ANY,ANY,numeric,numeric-method histL,Factorization-method plotL plotL,Factorization,numeric,ANY,ANY,character,numeric,numeric,character,numeric-method plotL,Factorization-method toolsFactorizationClass topLZ topLZ,Factorization,numeric,character,logical,ANY,ANY-method topLZ,Factorization,numeric,character,logical,ANY-method topLZ,Factorization,numeric,character,logical-method topLZ,Factorization-method |
| Converting genotyping data from 'vcf' to sparse matrix format | vcftoFABIA |
