Package: pedtools 2.7.1

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:Magnus Dehli Vigeland [aut, cre]

pedtools_2.7.1.tar.gz
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pedtools_2.7.1.tgz(r-4.4-any)pedtools_2.7.1.tgz(r-4.3-any)
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pedtools.pdf |pedtools.html
pedtools/json (API)
NEWS

# Install 'pedtools' in R:
install.packages('pedtools', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/magnusdv/pedtools/issues

On CRAN:

8.60 score 24 stars 18 packages 41 scripts 799 downloads 153 exports 10 dependencies

Last updated 3 months agofrom:fa784e1f06. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winOKNov 06 2024
R-4.5-linuxOKNov 06 2024
R-4.4-winOKNov 06 2024
R-4.4-macOKNov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:.annotatePed.drawPed.pedAlignment.pedAnnotation.pedScalingaddAlleleaddChildaddChildrenaddDaughteraddMarkeraddMarkersaddParentsaddSonafreqafreq<-allelesallowsMutationsancestorsancestralPedas_kinship2_pedigreeas.pedavuncularPedbranchbreakLoopschildrenchromchrom<-commonAncestorscommonDescendantsconnectedComponentscousinPeddescendantsdescentPathsdistributeMarkersdoubleCousinsdoubleFirstCousinsdrawPedemptyMarkerfamidfamid<-fatherfemalesfindLoopBreakersfindLoopBreakers2founderInbreedingfounderInbreeding<-foundersfoundersFirstfullSibMatinggenerationsgenotypegenotype<-getAllelesgetComponentgetFreqDatabasegetGenotypesgetLocusAttributesgetMapgetMarkersgetSexgrandparentshalfCousinPedhalfSibPedhalfSibStackhalfSibTrianglehasCommonAncestorhasInbredFoundershasLinkedMarkershasMarkershasParentsBeforeChildrenhasSelfinghasUnbrokenLoopsinbreedingLoopsinternalIDis.markeris.markerListis.pedis.pedListis.singletonisXmarkerleaveslinearPedmalesmarkermaskPedmendelianCheckmergePedmothermutmodmutmod<-nAllelesnamename<-nephews_niecesnewMarkernewPednMarkersnonfoundersnTypednuclearPedoffspringparentsparentsBeforeChildrenpedpedsizepeelingOrderplotPedListposMbposMb<-quadHalfFirstCousinsrandomPedreadFreqDatabasereadPedrelabelremoveIndividualsremoveMarkersreorderPedrestorePedselectMarkersselfingPedsetAfreqsetAlleleLabelssetAllelessetChromsetFounderInbreedingsetFreqDatabasesetGenotypesetLocusAttributessetMapsetMarkernamesetMarkerssetMutmodsetPositionsetSexsetSNPssiblingssingletonsingletonssortGenotypesspousessubnucsswapGenotypesswapSextieLoopstransferMarkerstypedMembersunmaskPedunrelateduntypedMembersvalidatePedwhichMarkerswriteFreqDatabasewritePed

Dependencies:evaluatehighrkinship2knitrlatticeMatrixpedmutquadprogxfunyaml

Introduction to the pedtools package

Rendered frompedtools.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-03-17
Started: 2018-07-26

Readme and manuals

Help Manual

Help pageTopics
Add alleleaddAllele
Convert pedigree to kinship2 formatas_kinship2_pedigree
Convert ped to data.frameas.data.frame.ped
Convert 'ped' to matrixas.matrix.ped restorePed
Conversions to ped objectsas.ped as.ped.data.frame
Connected pedigree componentsconnectedComponents
Distribute markers evenly along a set of chromosomesdistributeMarkers
Family identifierfamid famid.ped famid<- famid<-.ped
Inbreeding coefficients of foundersfounderInbreeding founderInbreeding<- setFounderInbreeding
Allele frequency databasefreqDatabase getFreqDatabase readFreqDatabase setFreqDatabase writeFreqDatabase
Allele matrix manipulationgetAlleles setAlleles
Pedigree componentgetComponent
Genotype matrixgetGenotypes
Tabulate marker positionsgetMap hasLinkedMarkers setMap
Get or set the sex of pedigree membersgetSex setSex swapSex
Pedigree loopsbreakLoops findLoopBreakers findLoopBreakers2 inbreedingLoops tieLoops
Test if something is a markeris.marker is.markerList
Is an object a 'ped' object?is.ped is.pedList is.singleton
Get or set locus attributesgetLocusAttributes locusAttributes setLocusAttributes
Marker objectsaddMarker marker
Attach markers to pedigreesaddMarkers marker_attach setMarkers
Get marker attributesafreq 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 attributesafreq<- 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 propertiesallowsMutations 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 markersgetMarkers marker_select removeMarkers selectMarkers whichMarkers
Set marker attributesmarker_setattr setAfreq setAlleleLabels setChrom setGenotype setMarkername setPosition
Mask and unmask pedigree datasetsmaskPed unmaskPed
Check for Mendelian errorsmendelianCheck
Merge two pedigreesmergePed
Internal marker constructornewMarker
Internal ped constructornewPed
The number of markers attached to a pedigreehasMarkers nMarkers
Pedigree constructionped singleton singletons
Create simple pedigreesancestralPed avuncularPed cousinPed halfCousinPed halfSibPed linearPed nuclearPed ped_basic selfingPed
Complex pedigree structuresdoubleCousins doubleFirstCousins fullSibMating halfSibStack halfSibTriangle ped_complex quadHalfFirstCousins
Internal ordering of pedigree membersfoundersFirst hasParentsBeforeChildren internalID parentsBeforeChildren ped_internal reorderPed
Add/remove pedigree membersaddChild addChildren addDaughter addParents addSon branch ped_modify removeIndividuals subset.ped
Pedigree subgroupsancestors children commonAncestors commonDescendants descendants descentPaths father females founders grandparents leaves males mother nephews_nieces nonfounders offspring parents ped_subgroups siblings spouses typedMembers unrelated untypedMembers
Pedigree utilitiesgenerations hasCommonAncestor hasInbredFounders hasSelfing hasUnbrokenLoops pedsize ped_utils peelingOrder subnucs
Plot pedigreedrawPed plot.list plot.ped plot.pedList
Internal plot methods.annotatePed .drawPed .pedAlignment .pedAnnotation .pedScaling plotmethods
Plot a collection of pedigrees.plotPedList
S3 methodsprint.nucleus
Printing pedigreesprint.ped
Random pedigreerandomPed
Read a pedigree from filereadPed
Get or modify pedigree labelslabels.list labels.ped relabel
Set a mutation modelsetMutmod
Attach SNP loci to a pedigreesetSNPs
Sort the alleles in each genotypesortGenotypes
Swap genotypes between individualsswapGenotypes
Transfer marker datatransferMarkers
Pedigree errorsvalidatePed
Write a pedigree to filewritePed