R: Creating and Working with Pedigrees and Marker Data

# Creating and Working with Pedigrees and Marker Data

## Documentation for package ‘pedtools’ version 2.10.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I L M N 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
addSibling | 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 basic 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 basic 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 basic 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
expectedHeterozygosity | Expected homozygosity and heterozygosity
expectedHomozygosity | Expected homozygosity and heterozygosity
extractSingletons | Extract singletons from pedigree

## -- 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 basic pedigrees
halfSibPed | Create basic pedigrees
halfSibStack | Complex pedigree structures
halfSibTriangle | Complex pedigree structures
harmoniseMarkers | Harmonise markers across components in a ped list
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
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?
isHomozygous | Find homozygous genotypes
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 basic 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
nChildren | Pedigree utilities
nephews_nieces | Pedigree subgroups
newMarker | Internal marker constructor
newPed | Internal ped constructor
niblings | Pedigree subgroups
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 basic pedigrees

## -- P --

parents | Pedigree subgroups
parentsBeforeChildren | Internal ordering of pedigree members
ped | Pedigree construction
pedsize | Pedigree utilities
ped_basic | Create basic 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
piblings | Pedigree subgroups
plot.list | Plot pedigree
plot.ped | Plot pedigree
plot.pedList | Plot pedigree
plotmethods | Internal plot methods
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
removeGenotypes | Allele matrix manipulation
removeIndividuals | Add/remove pedigree members
removeMarkers | Select or remove attached markers
reorderPed | Internal ordering of pedigree members
restorePed | Convert 'ped' to matrix

## -- S --

sameGenotype | Find markers for which two individuals have the same genotype
selectMarkers | Select or remove attached markers
selfingPed | Create basic 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
swapGenotypes | Swap genotypes between individuals
swapSex | Get or set the sex of pedigree members

## -- T --

tieLoops | Pedigree loops
transferMarkers | Transfer marker data
trim | Add/remove pedigree members
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