Creating and Working with Pedigrees and Marker Data
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Documentation for package ‘pedtools’ version 2.6.0
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A B C D E F G H I L M N O P Q R S T U V W misc
-- A --
| addAllele | Add allele |
| addChild | Add/remove pedigree members |
| addChildren | Add/remove pedigree members |
| addDaughter | Add/remove pedigree members |
| addMarker | Marker objects |
| addMarkers | Attach markers to pedigrees |
| addParents | Add/remove pedigree members |
| addSon | Add/remove pedigree members |
| afreq | Get marker attributes |
| afreq.list | Get marker attributes |
| afreq.marker | Get marker attributes |
| afreq.ped | Get marker attributes |
| afreq<- | Set marker attributes |
| afreq<-.list | Set marker attributes |
| afreq<-.marker | Set marker attributes |
| afreq<-.ped | Set marker attributes |
| alleles | Get marker attributes |
| alleles.list | Get marker attributes |
| alleles.marker | Get marker attributes |
| alleles.ped | Get marker attributes |
| allowsMutations | Marker properties |
| allowsMutations.default | Marker properties |
| allowsMutations.list | Marker properties |
| allowsMutations.marker | Marker properties |
| allowsMutations.ped | Marker properties |
| ancestors | Pedigree subgroups |
| ancestralPed | Create simple pedigrees |
| as.data.frame.ped | Convert ped to data.frame |
| as.matrix.ped | Convert 'ped' to matrix |
| as.ped | Conversions to ped objects |
| as.ped.data.frame | Conversions to ped objects |
| as_kinship2_pedigree | Convert pedigree to kinship2 format |
| avuncularPed | Create simple pedigrees |
-- B --
| branch | Add/remove pedigree members |
| breakLoops | Pedigree loops |
-- C --
| children | Pedigree subgroups |
| chrom | Get marker attributes |
| chrom.list | Get marker attributes |
| chrom.marker | Get marker attributes |
| chrom.ped | Get marker attributes |
| chrom<- | Set marker attributes |
| chrom<-.list | Set marker attributes |
| chrom<-.marker | Set marker attributes |
| chrom<-.ped | Set marker attributes |
| commonAncestors | Pedigree subgroups |
| commonDescendants | Pedigree subgroups |
| connectedComponents | Connected pedigree components |
| cousinPed | Create simple pedigrees |
-- D --
| descendants | Pedigree subgroups |
| descentPaths | Pedigree subgroups |
| distributeMarkers | Distribute markers evenly along a set of chromosomes |
| doubleCousins | Complex pedigree structures |
| doubleFirstCousins | Complex pedigree structures |
| drawPed | Plot pedigree |
-- E --
| emptyMarker | Marker properties |
| emptyMarker.default | Marker properties |
| emptyMarker.list | Marker properties |
| emptyMarker.marker | Marker properties |
| emptyMarker.ped | Marker properties |
-- F --
| famid | Family identifier |
| famid.ped | Family identifier |
| famid<- | Family identifier |
| famid<-.ped | Family identifier |
| father | Pedigree subgroups |
| females | Pedigree subgroups |
| findLoopBreakers | Pedigree loops |
| findLoopBreakers2 | Pedigree loops |
| founderInbreeding | Inbreeding coefficients of founders |
| founderInbreeding<- | Inbreeding coefficients of founders |
| founders | Pedigree subgroups |
| foundersFirst | Internal ordering of pedigree members |
| freqDatabase | Allele frequency database |
| fullSibMating | Complex pedigree structures |
-- G --
| generations | Pedigree utilities |
| genotype | Get marker attributes |
| genotype.marker | Get marker attributes |
| genotype.ped | Get marker attributes |
| genotype<- | Set marker attributes |
| genotype<-.marker | Set marker attributes |
| genotype<-.ped | Set marker attributes |
| getAlleles | Allele matrix manipulation |
| getComponent | Pedigree component |
| getFreqDatabase | Allele frequency database |
| getGenotypes | Genotype matrix |
| getLocusAttributes | Get or set locus attributes |
| getMap | Tabulate marker positions |
| getMarkers | Select or remove attached markers |
| getSex | Get or set the sex of pedigree members |
| grandparents | Pedigree subgroups |
-- H --
| halfCousinPed | Create simple pedigrees |
| halfSibPed | Create simple pedigrees |
| halfSibStack | Complex pedigree structures |
| halfSibTriangle | Complex pedigree structures |
| hasCommonAncestor | Pedigree utilities |
| hasInbredFounders | Pedigree utilities |
| hasLinkedMarkers | Tabulate marker positions |
| hasMarkers | The number of markers attached to a pedigree |
| hasParentsBeforeChildren | Internal ordering of pedigree members |
| hasSelfing | Pedigree utilities |
| hasUnbrokenLoops | Pedigree utilities |
-- I --
| inbreedingLoops | Pedigree loops |
| internalID | Internal ordering of pedigree members |
| internalplot | Internal plot methods |
| is.marker | Test if something is a marker |
| is.markerList | Test if something is a marker |
| is.ped | Is an object a 'ped' object? |
| is.pedList | Is an object a 'ped' object? |
| is.singleton | Is an object a 'ped' object? |
| isXmarker | Marker properties |
| isXmarker.default | Marker properties |
| isXmarker.list | Marker properties |
| isXmarker.marker | Marker properties |
| isXmarker.ped | Marker properties |
-- L --
| labels.list | Get or modify pedigree labels |
| labels.ped | Get or modify pedigree labels |
| leaves | Pedigree subgroups |
| linearPed | Create simple pedigrees |
| locusAttributes | Get or set locus attributes |
-- M --
| males | Pedigree subgroups |
| marker | Marker objects |
| marker_attach | Attach markers to pedigrees |
| marker_getattr | Get marker attributes |
| marker_inplace | Set marker attributes |
| marker_prop | Marker properties |
| marker_select | Select or remove attached markers |
| marker_setattr | Set marker attributes |
| maskPed | Mask and unmask pedigree datasets |
| mendelianCheck | Check for Mendelian errors |
| mergePed | Merge two pedigrees |
| mother | Pedigree subgroups |
| mutmod | Get marker attributes |
| mutmod.list | Get marker attributes |
| mutmod.marker | Get marker attributes |
| mutmod.ped | Get marker attributes |
| mutmod<- | Set marker attributes |
| mutmod<-.list | Set marker attributes |
| mutmod<-.marker | Set marker attributes |
| mutmod<-.ped | Set marker attributes |
-- N --
| nAlleles | Marker properties |
| nAlleles.default | Marker properties |
| nAlleles.list | Marker properties |
| nAlleles.marker | Marker properties |
| nAlleles.ped | Marker properties |
| name | Get marker attributes |
| name.list | Get marker attributes |
| name.marker | Get marker attributes |
| name.ped | Get marker attributes |
| name<- | Set marker attributes |
| name<-.list | Set marker attributes |
| name<-.marker | Set marker attributes |
| name<-.ped | Set marker attributes |
| nephews_nieces | Pedigree subgroups |
| newMarker | Internal marker constructor |
| newPed | Internal ped constructor |
| nMarkers | The number of markers attached to a pedigree |
| nonfounders | Pedigree subgroups |
| nTyped | Marker properties |
| nTyped.default | Marker properties |
| nTyped.list | Marker properties |
| nTyped.marker | Marker properties |
| nTyped.ped | Marker properties |
| nuclearPed | Create simple pedigrees |
-- O --
| offspring | Pedigree subgroups |
-- P --
| parents | Pedigree subgroups |
| parentsBeforeChildren | Internal ordering of pedigree members |
| ped | Pedigree construction |
| pedsize | Pedigree utilities |
| ped_basic | Create simple pedigrees |
| ped_complex | Complex pedigree structures |
| ped_internal | Internal ordering of pedigree members |
| ped_modify | Add/remove pedigree members |
| ped_subgroups | Pedigree subgroups |
| ped_utils | Pedigree utilities |
| peelingOrder | Pedigree utilities |
| plot.list | Plot pedigree |
| plot.ped | Plot pedigree |
| plot.pedList | Plot pedigree |
| plotPedList | Plot a collection of pedigrees. |
| posMb | Get marker attributes |
| posMb.marker | Get marker attributes |
| posMb.ped | Get marker attributes |
| posMb<- | Set marker attributes |
| posMb<-.marker | Set marker attributes |
| posMb<-.ped | Set marker attributes |
| print.nucleus | S3 methods |
| print.ped | Printing pedigrees |
-- Q --
| quadHalfFirstCousins | Complex pedigree structures |
-- R --
| randomPed | Random pedigree |
| readFreqDatabase | Allele frequency database |
| readPed | Read a pedigree from file |
| relabel | Get or modify pedigree labels |
| removeIndividuals | Add/remove pedigree members |
| removeMarkers | Select or remove attached markers |
| reorderPed | Internal ordering of pedigree members |
| restorePed | Convert 'ped' to matrix |
-- S --
| selectMarkers | Select or remove attached markers |
| selfingPed | Create simple pedigrees |
| setAfreq | Set marker attributes |
| setAlleleLabels | Set marker attributes |
| setAlleles | Allele matrix manipulation |
| setChrom | Set marker attributes |
| setFounderInbreeding | Inbreeding coefficients of founders |
| setFreqDatabase | Allele frequency database |
| setGenotype | Set marker attributes |
| setLocusAttributes | Get or set locus attributes |
| setMap | Tabulate marker positions |
| setMarkername | Set marker attributes |
| setMarkers | Attach markers to pedigrees |
| setMutmod | Set a mutation model |
| setPosition | Set marker attributes |
| setSex | Get or set the sex of pedigree members |
| setSNPs | Attach SNP loci to a pedigree |
| siblings | Pedigree subgroups |
| singleton | Pedigree construction |
| singletons | Pedigree construction |
| sortGenotypes | Sort the alleles in each genotype |
| spouses | Pedigree subgroups |
| subnucs | Pedigree utilities |
| subset.ped | Add/remove pedigree members |
| swapSex | Get or set the sex of pedigree members |
-- T --
| tieLoops | Pedigree loops |
| transferMarkers | Transfer marker data |
| typedMembers | Pedigree subgroups |
-- U --
| unmaskPed | Mask and unmask pedigree datasets |
| unrelated | Pedigree subgroups |
| untypedMembers | Pedigree subgroups |
-- V --
| validatePed | Pedigree errors |
-- W --
| whichMarkers | Select or remove attached markers |
| writeFreqDatabase | Allele frequency database |
| writePed | Write a pedigree to file |
-- misc --
| .annotatePed | Internal plot methods |
| .drawPed | Internal plot methods |
| .pedAlignment | Internal plot methods |
| .pedAnnotation | Internal plot methods |
| .pedScaling | Internal plot methods |