Creating and Working with Pedigrees and Marker Data


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Documentation for package ‘pedtools’ version 1.0.1

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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

-- A --

addChildren Add/remove pedigree members
addDaughter Add/remove pedigree members
addMarkers Attach markers to pedigrees
addParents Add/remove pedigree members
addSon Add/remove pedigree members
afreq Get/set marker attributes
afreq.list Get/set marker attributes
afreq.marker Get/set marker attributes
afreq.ped Get/set marker attributes
afreq<- Get/set marker attributes
afreq<-.list Get/set marker attributes
afreq<-.marker Get/set marker attributes
afreq<-.ped Get/set marker attributes
alleles Get/set marker attributes
alleles.list Get/set marker attributes
alleles.marker Get/set marker attributes
alleles.ped Get/set 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 Plot pedigrees with genotypes

-- B --

branch Add/remove pedigree members
breakLoops Pedigree loops

-- C --

children Pedigree subgroups
chrom Get/set marker attributes
chrom.list Get/set marker attributes
chrom.marker Get/set marker attributes
chrom.ped Get/set marker attributes
chrom<- Get/set marker attributes
chrom<-.list Get/set marker attributes
chrom<-.marker Get/set marker attributes
chrom<-.ped Get/set marker attributes
commonAncestors Pedigree subgroups
commonDescendants Pedigree subgroups
connectedComponents Connected pedigree components
cousinPed Create simple pedigrees

-- D --

descendants Pedigree subgroups
doubleCousins Complex pedigree structures
doubleFirstCousins Complex pedigree structures

-- 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/set marker attributes
genotype.marker Get/set marker attributes
genotype.ped Get/set marker attributes
genotype<- Get/set marker attributes
genotype<-.marker Get/set marker attributes
genotype<-.ped Get/set marker attributes
getAlleles Allele matrix manipulation
getComponent Pedigree component
getFreqDatabase Allele frequency database
getFrequencyDatabase 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
hasCommonAncestor Pedigree utilities
hasInbredFounders Pedigree utilities
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?
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_getset Get/set marker attributes
marker_prop Marker properties
marker_select Select or remove attached markers
mendelianCheck Check for Mendelian errors
mergePed Merge two pedigrees
mother Pedigree subgroups
mutmod Get/set marker attributes
mutmod.list Get/set marker attributes
mutmod.marker Get/set marker attributes
mutmod.ped Get/set marker attributes
mutmod<- Get/set marker attributes
mutmod<-.list Get/set marker attributes
mutmod<-.marker Get/set marker attributes
mutmod<-.ped Get/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/set marker attributes
name.list Get/set marker attributes
name.marker Get/set marker attributes
name.ped Get/set marker attributes
name<- Get/set marker attributes
name<-.list Get/set marker attributes
name<-.marker Get/set marker attributes
name<-.ped Get/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
pedtools pedtools: Tools for working with pedigrees in R
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.ped Plot pedigrees with genotypes
plot.pedList Plot pedigrees with genotypes
plot.singleton Plot pedigrees with genotypes
plotPedList Plot a collection of pedigrees.
posMb Get/set marker attributes
posMb.marker Get/set marker attributes
posMb.ped Get/set marker attributes
posMb<- Get/set marker attributes
posMb<-.marker Get/set marker attributes
posMb<-.ped Get/set marker attributes
print.nucleus S3 methods
print.ped Printing pedigrees

-- Q --

quadHalfFirstCousins Complex pedigree structures

-- R --

randomPed Random pedigree
readFreqDatabase Allele frequency database
readFrequencyDatabase 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
setAlleles Allele matrix manipulation
setFreqDatabase Allele frequency database
setFrequencyDatabase Allele frequency database
setLocusAttributes Get or set locus attributes
setMap Tabulate marker positions
setMarkers Attach markers to pedigrees
setSex Get or set the sex of pedigree members
siblings Pedigree subgroups
singleton 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 --

unrelated Pedigree subgroups
untypedMembers Pedigree subgroups

-- V --

validatePed Pedigree errors

-- W --

whichMarkers Select or remove attached markers
writeFreqDatabase Allele frequency database
writeFrequencyDatabase Allele frequency database
writePed Write a pedigree to file