Installation | Introduction | The demo data set of genotyping results | Format the genotype | Find outlier samples/markers | Find sample duplicates | Count crossovers | Calculate genetic distance | Calculate genetic distance for equally binned intervals | Total genetic distances | Plotting genetic distance for each bin | Plot cumulative distances | Whole Genome Genetic distances Plot | Sessioninfo
Package: comapr 1.17.0
Ruqian Lyu
comapr: Crossover analysis and genetic map construction
comapr detects crossover intervals for single gametes from their haplotype states sequences and stores the crossovers in GRanges object. The genetic distances can then be calculated via the mapping functions using estimated crossover rates for maker intervals. Visualisation functions for plotting interval-based genetic map or cumulative genetic distances are implemented, which help reveal the variation of crossovers landscapes across the genome and across individuals.
Authors:
comapr_1.17.0.tar.gz
comapr_1.17.0.zip(r-4.7)comapr_1.17.0.zip(r-4.6)comapr_1.17.0.zip(r-4.5)
comapr_1.17.0.tgz(r-4.6-any)comapr_1.17.0.tgz(r-4.5-any)
comapr_1.17.0.tar.gz(r-4.7-any)comapr_1.17.0.tar.gz(r-4.6-any)
comapr_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
comapr/json (API)
| # Install 'comapr' in R: |
| install.packages('comapr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- coCount - RangedSummarizedExperiment object containing the crossover counts across samples for the list of SNP marker intervals
- parents_geno - Parents' genotype for F1 samples in 'snp_geno'
- snp_geno - Markers by genotype results for a group of samples
- snp_geno_gr - Markers by genotype results for a group of samples
- twoSamples - RangedSummarizedExperiment object containing the Viterbi states SNP markers for samples from two groups. 'colData(twoSamples)' contains the sample group factor.
On BioConductor:comapr-1.17.0(bioc 3.24)comapr-1.16.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwaresinglecellvisualizationgenetics
Last updated from:b210ba9245. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 282 | ||
| linux-devel-x86_64 | NOTE | 542 | ||
| source / vignettes | OK | 359 | ||
| linux-release-x86_64 | NOTE | 568 | ||
| macos-release-arm64 | NOTE | 269 | ||
| macos-oldrel-arm64 | NOTE | 236 | ||
| windows-devel | NOTE | 494 | ||
| windows-release | NOTE | 548 | ||
| windows-oldrel | NOTE | 471 | ||
| wasm-release | OK | 216 |
Exports:bootstrapDistcalGeneticDistcombineHapStatecorrectGTcountBinStatecountCOscountGTfilterGTfindDupSamplesgetAFTracksgetCellAFTrackgetCellCORangegetCellDPTrackgetDistortedMarkersgetMeanDPTrackgetSNPDensityTrackperCellChrQCpermuteDistperSegChrQCplotCountplotGeneticDistplotGTFreqplotWholeGenomereadColMMreadHapState
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocirclizecliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2GlobalOptionsgluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslotelpillarpkgconfigplotlyplyrpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml
Genetic distance calculation from genotype shifts of markers
Last update: 2021-12-31
Started: 2020-10-13
single-sperm-co-analysis
Introduction | Locate file path | File information | Diagnostic functions | perCellChrQC | Input parsing | Construct RangedSummarizedExpriment object | Formate sample group factor | Add sample group factor | Combine two groups | Count crossovers | Count crossovers for SNP intervals | Calculate genetic distances | Plot whole genome genetic distances | Group differences | Session info
Last update: 2021-09-26
Started: 2021-01-21
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| bootstrapDist | bootstrapDist |
| calGeneticDist | calGeneticDist calGeneticDist,GRanges,missing,ANY,ANY,character-method calGeneticDist,GRanges,missing,ANY,ANY,missing-method calGeneticDist,GRanges,numeric,ANY,ANY,character-method calGeneticDist,GRanges,numeric,ANY,ANY,missing-method calGeneticDist,RangedSummarizedExperiment,missing,ANY,ANY,character-method calGeneticDist,RangedSummarizedExperiment,missing,ANY,ANY,missing-method calGeneticDist,RangedSummarizedExperiment,numeric,ANY,ANY,character-method calGeneticDist,RangedSummarizedExperiment,numeric,ANY,ANY,missing-method |
| RangedSummarizedExperiment object containing the crossover counts across samples for the list of SNP marker intervals | coCount |
| 'comapr' package | comapr |
| combineHapState | combineHapState |
| correctGT | correctGT |
| countBinState | countBinState |
| countCOs | countCOs countCOs,GRanges-method countCOs,RangedSummarizedExperiment-method |
| countGT | countGT |
| filterGT | filterGT filterGT,GRanges,numeric,numeric-method filterGT,matrix,numeric,numeric-method |
| findDupSamples | findDupSamples |
| getAFTracks | getAFTracks |
| getCellAFTrack Generates the DataTracks for plotting AF and crossover regions | getCellAFTrack |
| getCellCORange | getCellCORange |
| getCellDPTrack Generates the DataTrack for plotting DP of a selected cell | getCellDPTrack |
| getDistortedMarkers | getDistortedMarkers |
| getMeanDPTrack | getMeanDPTrack |
| getSNPDensityTrack | getSNPDensityTrack |
| Parents' genotype for F1 samples in `snp_geno` | parents_geno |
| perCellChrQC | perCellChrQC |
| permuteDist | permuteDist |
| perSegChrQC | perSegChrQC |
| plotCount | plotCount plotCount,GRanges,logical,character-method plotCount,GRanges,logical,missing-method plotCount,GRanges,missing,character-method plotCount,GRanges,missing,missing-method plotCount,RangedSummarizedExperiment,logical,character-method plotCount,RangedSummarizedExperiment,logical,missing-method plotCount,RangedSummarizedExperiment,missing,character-method plotCount,RangedSummarizedExperiment,missing,missing-method |
| plotGeneticDist | plotGeneticDist |
| plotGTFreq | plotGTFreq |
| Plot cumulative genetic distances across the genome | plotWholeGenome |
| readColMM | readColMM |
| readHapState | readHapState |
| Markers by genotype results for a group of samples | snp_geno |
| Markers by genotype results for a group of samples | snp_geno_gr |
| RangedSummarizedExperiment object containing the Viterbi states SNP markers for samples from two groups. `colData(twoSamples)` contains the sample group factor. | twoSamples |
