Package: pedtools 2.10.0.9000
Magnus Dehli Vigeland
pedtools: Creating and Working with Pedigrees and Marker Data
A comprehensive collection of tools for creating, manipulating and visualising pedigrees and genetic marker data. Pedigrees can be read from text files or created on the fly with built-in functions. A range of utilities enable modifications like adding or removing individuals, breaking loops, and merging pedigrees. An online tool for creating pedigrees interactively, based on 'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>. 'pedtools' is the hub of the 'pedsuite', a collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite' is given in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).
Authors:
pedtools_2.10.0.9000.tar.gz
pedtools_2.10.0.9000.zip(r-4.7)pedtools_2.10.0.9000.zip(r-4.6)pedtools_2.10.0.9000.zip(r-4.5)
pedtools_2.10.0.9000.tgz(r-4.6-any)pedtools_2.10.0.9000.tgz(r-4.5-any)
pedtools_2.10.0.9000.tar.gz(r-4.7-any)pedtools_2.10.0.9000.tar.gz(r-4.6-any)
pedtools_2.10.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pedtools/json (API)
NEWS
| # Install 'pedtools' in R: |
| install.packages('pedtools', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/magnusdv/pedtools/issues
Pkgdown/docs site:https://magnusdv.github.io
Last updated from:659b0b2595. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 167 | ||
| source / vignettes | OK | 182 | ||
| linux-release-x86_64 | OK | 167 | ||
| macos-release-arm64 | OK | 103 | ||
| macos-oldrel-arm64 | OK | 110 | ||
| windows-devel | OK | 118 | ||
| windows-release | OK | 114 | ||
| windows-oldrel | OK | 106 | ||
| wasm-release | OK | 108 |
Exports:.annotatePed.drawPed.pedAlignment.pedAnnotation.pedScalingaddAlleleaddChildaddChildrenaddDaughteraddMarkeraddMarkersaddParentsaddSiblingaddSonafreqafreq<-allelesallowsMutationsancestorsancestralPedas_kinship2_pedigreeas.pedavuncularPedbranchbreakLoopschildrenchromchrom<-commonAncestorscommonDescendantsconnectedComponentscousinPeddescendantsdescentPathsdistributeMarkersdoubleCousinsdoubleFirstCousinsdrawPedemptyMarkerexpectedHeterozygosityexpectedHomozygosityextractSingletonsfamidfamid<-fatherfemalesfindLoopBreakersfindLoopBreakers2founderInbreedingfounderInbreeding<-foundersfoundersFirstfullSibMatinggenerationsgenotypegenotype<-getAllelesgetComponentgetFreqDatabasegetGenotypesgetLocusAttributesgetMapgetMarkersgetSexgrandparentshalfCousinPedhalfSibPedhalfSibStackhalfSibTriangleharmoniseMarkershasCommonAncestorhasInbredFoundershasLinkedMarkershasMarkershasParentsBeforeChildrenhasSelfinghasUnbrokenLoopsinbreedingLoopsinternalIDis.markeris.markerListis.pedis.pedListis.singletonisHomozygousisXmarkerleaveslinearPedmalesmarkermaskPedmendelianCheckmergePedmothermutmodmutmod<-nAllelesnamename<-nChildrennephews_niecesnewMarkernewPedniblingsnMarkersnonfoundersnTypednuclearPedparentsparentsBeforeChildrenpedpedsizepeelingOrderpiblingsplotPedListposMbposMb<-quadHalfFirstCousinsrandomPedreadFreqDatabasereadPedrelabelremoveGenotypesremoveIndividualsremoveMarkersreorderPedrestorePedsameGenotypeselectMarkersselfingPedsetAfreqsetAlleleLabelssetAllelessetChromsetFounderInbreedingsetFreqDatabasesetGenotypesetLocusAttributessetMapsetMarkernamesetMarkerssetMutmodsetPositionsetSexsetSNPssiblingssingletonsingletonssortGenotypesspousessubnucsswapGenotypesswapSextieLoopstransferMarkerstrimtypedMembersunmaskPedunrelateduntypedMembersvalidatePedwhichMarkerswriteFreqDatabasewritePed
Dependencies:evaluatehighrkinship2knitrlatticelpSolveMatrixpedmutquadprogxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add allele | addAllele |
| Convert pedigree to kinship2 format | as_kinship2_pedigree |
| Convert ped to data.frame | as.data.frame.ped |
| Convert 'ped' to matrix | as.matrix.ped restorePed |
| Conversions to ped objects | as.ped as.ped.data.frame |
| Connected pedigree components | connectedComponents |
| Distribute markers evenly along a set of chromosomes | distributeMarkers |
| Expected homozygosity and heterozygosity | expectedHeterozygosity expectedHomozygosity |
| Extract singletons from pedigree | extractSingletons |
| Family identifier | famid famid.ped famid<- famid<-.ped |
| Inbreeding coefficients of founders | founderInbreeding founderInbreeding<- setFounderInbreeding |
| Allele frequency database | freqDatabase getFreqDatabase readFreqDatabase setFreqDatabase writeFreqDatabase |
| Allele matrix manipulation | getAlleles removeGenotypes setAlleles |
| Pedigree component | getComponent |
| Genotype matrix | getGenotypes |
| Tabulate marker positions | getMap hasLinkedMarkers setMap |
| Get or set the sex of pedigree members | getSex setSex swapSex |
| Harmonise markers across components in a ped list | harmoniseMarkers |
| Pedigree loops | breakLoops findLoopBreakers findLoopBreakers2 inbreedingLoops tieLoops |
| Test if something is a marker | is.marker is.markerList |
| Is an object a 'ped' object? | is.ped is.pedList is.singleton |
| Find homozygous genotypes | isHomozygous |
| Get or set locus attributes | getLocusAttributes locusAttributes setLocusAttributes |
| Marker objects | addMarker marker |
| Attach markers to pedigrees | addMarkers marker_attach setMarkers |
| Get marker attributes | afreq afreq.list afreq.marker afreq.ped alleles alleles.list alleles.marker alleles.ped chrom chrom.list chrom.marker chrom.ped genotype genotype.marker genotype.ped marker_getattr mutmod mutmod.list mutmod.marker mutmod.ped name name.list name.marker name.ped posMb posMb.marker posMb.ped |
| Set marker attributes | afreq<- afreq<-.list afreq<-.marker afreq<-.ped chrom<- chrom<-.list chrom<-.marker chrom<-.ped genotype<- genotype<-.marker genotype<-.ped marker_inplace mutmod<- mutmod<-.list mutmod<-.marker mutmod<-.ped name<- name<-.list name<-.marker name<-.ped posMb<- posMb<-.marker posMb<-.ped |
| Marker properties | allowsMutations allowsMutations.default allowsMutations.list allowsMutations.marker allowsMutations.ped emptyMarker emptyMarker.default emptyMarker.list emptyMarker.marker emptyMarker.ped isXmarker isXmarker.default isXmarker.list isXmarker.marker isXmarker.ped marker_prop nAlleles nAlleles.default nAlleles.list nAlleles.marker nAlleles.ped nTyped nTyped.default nTyped.list nTyped.marker nTyped.ped |
| Select or remove attached markers | getMarkers marker_select removeMarkers selectMarkers whichMarkers |
| Set marker attributes | marker_setattr setAfreq setAlleleLabels setChrom setGenotype setMarkername setPosition |
| Mask and unmask pedigree datasets | maskPed unmaskPed |
| Check for Mendelian errors | mendelianCheck |
| Merge two pedigrees | mergePed |
| Internal marker constructor | newMarker |
| Internal ped constructor | newPed |
| The number of markers attached to a pedigree | hasMarkers nMarkers |
| Pedigree construction | ped singleton singletons |
| Create basic pedigrees | ancestralPed avuncularPed cousinPed halfCousinPed halfSibPed linearPed nuclearPed ped_basic selfingPed |
| Complex pedigree structures | doubleCousins doubleFirstCousins fullSibMating halfSibStack halfSibTriangle ped_complex quadHalfFirstCousins |
| Internal ordering of pedigree members | foundersFirst hasParentsBeforeChildren internalID parentsBeforeChildren ped_internal reorderPed |
| Add/remove pedigree members | addChild addChildren addDaughter addParents addSibling addSon branch ped_modify removeIndividuals subset.ped trim |
| Pedigree subgroups | ancestors children commonAncestors commonDescendants descendants descentPaths father females founders grandparents leaves males mother nephews_nieces niblings nonfounders parents ped_subgroups piblings siblings spouses typedMembers unrelated untypedMembers |
| Pedigree utilities | generations hasCommonAncestor hasInbredFounders hasSelfing hasUnbrokenLoops nChildren pedsize ped_utils peelingOrder subnucs |
| Plot pedigree | drawPed plot.list plot.ped plot.pedList |
| Internal plot methods | .annotatePed .drawPed .pedAlignment .pedAnnotation .pedScaling plotmethods |
| Plot a collection of pedigrees. | plotPedList |
| S3 methods | print.nucleus |
| Printing pedigrees | print.ped |
| Random pedigree | randomPed |
| Read a pedigree from file | readPed |
| Get or modify pedigree labels | labels.list labels.ped relabel |
| Find markers for which two individuals have the same genotype | sameGenotype |
| Set a mutation model | setMutmod |
| Attach SNP loci to a pedigree | setSNPs |
| Sort the alleles in each genotype | sortGenotypes |
| Swap genotypes between individuals | swapGenotypes |
| Transfer marker data | transferMarkers |
| Pedigree errors | validatePed |
| Write a pedigree to file | writePed |