API for magnusdv/pedtools
Creating and Working with Pedigrees and Marker Data

Global functions
.addTxt	Source code
.alignDAG	Source code
.annotatePed	Man page Source code
.comb2	Source code
.drawPed	Man page Source code
.extendPlist	Source code
.fix34	Source code
.flipNames	Source code
.hasStepwiseModel	Source code
.isIntegral	Source code
.myintersect	Source code
.mysetdiff	Source code
.mysortInt	Source code
.pedAlignment	Man page Source code
.pedAnnotation	Man page Source code
.pedScaling	Man page Source code
.plotDAG	Source code
.prepLabs	Source code
.prepLabs2	Source code
.prepPlotarg	Source code
.rand01	Source code
.setSNPfreqs	Source code
.transferSimple	Source code
`%\|\|%`	Source code
`afreq<-.list`	Source code
`afreq<-.marker`	Source code
`afreq<-.ped`	Source code
`afreq<-`	Source code
`chrom<-.list`	Source code
`chrom<-.marker`	Source code
`chrom<-.ped`	Source code
`chrom<-`	Source code
`famid.ped`	Source code
`famid<-.ped`	Source code
`famid<-`	Source code
`famid`	Source code
`founderInbreeding<-`	Source code
`genotype<-.marker`	Source code
`genotype<-.ped`	Source code
`genotype<-`	Source code
`mutmod<-.list`	Source code
`mutmod<-.marker`	Source code
`mutmod<-.ped`	Source code
`mutmod<-`	Source code
`name<-.list`	Source code
`name<-.marker`	Source code
`name<-.ped`	Source code
`name<-`	Source code
`posMb<-.marker`	Source code
`posMb<-.ped`	Source code
`posMb<-`	Source code
addAllele	Man page Source code
addChild	Man page Source code
addChildren	Man page Source code
addDaughter	Man page Source code
addMarker	Man page Source code
addMarkers	Man page Source code
addParents	Man page Source code
addSon	Man page Source code
afreq	Man page Source code
afreq.list	Man page Source code
afreq.marker	Man page Source code
afreq.ped	Man page Source code
afreq<-	Man page
afreq<-.list	Man page
afreq<-.marker	Man page
afreq<-.ped	Man page
allelematrix2markerlist	Source code
alleles	Man page Source code
alleles.list	Man page Source code
alleles.marker	Man page Source code
alleles.ped	Man page Source code
allowsMutations	Man page Source code
allowsMutations.default	Man page Source code
allowsMutations.list	Man page Source code
allowsMutations.marker	Man page Source code
allowsMutations.ped	Man page Source code
ancestors	Man page Source code
ancestralPed	Man page Source code
any_self_ancestry	Source code
as.data.frame.ped	Man page Source code
as.matrix.ped	Man page Source code
as.ped	Man page Source code
as.ped.data.frame	Man page Source code
as_kinship2_pedigree	Man page Source code
avuncularPed	Man page Source code
branch	Man page Source code
breakLoops	Man page Source code
checkConsistency	Source code
checkDupNames	Source code
checkLocusAttribs	Source code
checkMutationMatrix	Source code
children	Man page Source code
chrom	Man page Source code
chrom.list	Man page Source code
chrom.marker	Man page Source code
chrom.ped	Man page Source code
chrom<-	Man page
chrom<-.list	Man page
chrom<-.marker	Man page
chrom<-.ped	Man page
commentAndRealign	Source code
commonAncestors	Man page Source code
commonDescendants	Man page Source code
connectedComponents	Man page Source code
cousinPed	Man page Source code
cousins	Source code
descendants	Man page Source code
descentPaths	Man page Source code
distributeMarkers	Man page Source code
doubleCousins	Man page Source code
doubleFirstCousins	Man page Source code
drawPed	Man page Source code
emptyMarker	Man page Source code
emptyMarker.default	Man page Source code
emptyMarker.list	Man page Source code
emptyMarker.marker	Man page Source code
emptyMarker.ped	Man page Source code
famid	Man page
famid.ped	Man page
famid<-	Man page
famid<-.ped	Man page
fast.grid	Source code
father	Man page Source code
females	Man page Source code
findLoopBreakers	Man page Source code
findLoopBreakers2	Man page Source code
fixMerlinMap	Source code
format.marker	Source code
founderInbreeding	Man page Source code
founderInbreeding<-	Man page
founders	Man page Source code
foundersFirst	Man page Source code
freqDatabase	Man page
freqDb2attribList	Source code
fullSibMating	Man page Source code
generateLabs	Source code
generations	Man page Source code
genotype	Man page Source code
genotype.marker	Man page Source code
genotype.ped	Man page Source code
genotype<-	Man page
genotype<-.marker	Man page
genotype<-.ped	Man page
getAlleles	Man page Source code
getComponent	Man page Source code
getFreqDatabase	Man page Source code
getGenotype	Source code
getGenotypeMarker	Source code
getGenotypes	Man page Source code
getLocusAttributes	Man page Source code
getMap	Man page Source code
getMarkers	Man page Source code
getSex	Man page Source code
glist2amat	Source code
grandparents	Man page Source code
halfCousinPed	Man page Source code
halfSibPed	Man page Source code
halfSibStack	Man page Source code
halfSibTriangle	Man page Source code
hasCommonAncestor	Man page Source code
hasInbredFounders	Man page Source code
hasLinkedMarkers	Man page Source code
hasMarkers	Man page Source code
hasNumLabs	Source code
hasParentsBeforeChildren	Man page Source code
hasSelfing	Man page Source code
hasUnbrokenLoops	Man page Source code
inbreedingLoops	Man page Source code
internalID	Man page Source code
internalplot	Man page
is.marker	Man page Source code
is.markerList	Man page Source code
is.ped	Man page Source code
is.pedList	Man page Source code
is.singleton	Man page Source code
isCount	Source code
isNumber	Source code
isXmarker	Man page Source code
isXmarker.default	Man page Source code
isXmarker.list	Man page Source code
isXmarker.marker	Man page Source code
isXmarker.ped	Man page Source code
labels.list	Man page Source code
labels.ped	Man page Source code
leaves	Man page Source code
linearPed	Man page Source code
listIdentical	Source code
locusAttributes	Man page
maleXCheck	Source code
maleXHomoz	Source code
males	Man page Source code
marker	Man page Source code
marker_attach	Man page
marker_getattr	Man page
marker_inplace	Man page
marker_prop	Man page
marker_select	Man page
marker_setattr	Man page
markerlist2allelematrix	Source code
maskPed	Man page Source code
mendelianCheck	Man page Source code
mergePed	Man page Source code
mother	Man page Source code
mutmod	Man page Source code
mutmod.list	Man page Source code
mutmod.marker	Man page Source code
mutmod.ped	Man page Source code
mutmod<-	Man page
mutmod<-.list	Man page
mutmod<-.marker	Man page
mutmod<-.ped	Man page
nAlleles	Man page Source code
nAlleles.default	Man page Source code
nAlleles.list	Man page Source code
nAlleles.marker	Man page Source code
nAlleles.ped	Man page Source code
nMarkers	Man page Source code
nTyped	Man page Source code
nTyped.default	Man page Source code
nTyped.list	Man page Source code
nTyped.marker	Man page Source code
nTyped.ped	Man page Source code
name	Man page Source code
name.list	Man page Source code
name.marker	Man page Source code
name.ped	Man page Source code
name2.ped	Source code
name<-	Man page
name<-.list	Man page
name<-.marker	Man page
name<-.ped	Man page
nephews_nieces	Man page Source code
newMarker	Man page Source code
newPed	Man page Source code
nextNN	Source code
nonfounders	Man page Source code
nuclearPed	Man page Source code
offspring	Man page
parents	Man page Source code
parentsBeforeChildren	Man page Source code
parseDots	Source code
parseGeno	Source code
ped	Man page Source code
ped_basic	Man page
ped_complex	Man page
ped_internal	Man page
ped_modify	Man page
ped_subgroups	Man page
ped_utils	Man page
pedsize	Man page Source code
pedtools	Man page
pedtools-package	Man page
peelingOrder	Man page Source code
plot.list	Man page Source code
plot.ped	Man page Source code
plot.pedList	Man page Source code
plotPedList	Man page Source code
posMb	Man page Source code
posMb.marker	Man page Source code
posMb.ped	Man page Source code
posMb<-	Man page
posMb<-.marker	Man page
posMb<-.ped	Man page
print.marker	Source code
print.nucleus	Man page Source code
print.ped	Man page Source code
quadHalfFirstCousins	Man page Source code
quadSecondCousins	Source code
questionMaleHetX	Source code
randomPed	Man page Source code
readFreqDatabase	Man page Source code
readPed	Man page Source code
relabel	Man page Source code
removeIndividuals	Man page Source code
removeMarkers	Man page Source code
reorderPed	Man page Source code
reorderSimple	Source code
restorePed	Man page Source code
safe_sample	Source code
selectMarkers	Man page Source code
selfingPed	Man page Source code
seq_markers	Source code
seq_ped	Source code
setAfreq	Man page Source code
setAlleleLabels	Man page Source code
setAlleles	Man page Source code
setChrom	Man page Source code
setFounderInbreeding	Man page Source code
setFreqDatabase	Man page Source code
setGenotype	Man page Source code
setGenotypeMarker	Source code
setLocusAttributes	Man page Source code
setMap	Man page Source code
setMarkername	Man page Source code
setMarkers	Man page Source code
setMutmod	Man page Source code
setPosition	Man page Source code
setSNPs	Man page Source code
setSex	Man page Source code
shortArrows	Source code
siblings	Man page Source code
sibshipCheck	Source code
singleton	Man page Source code
singletons	Man page Source code
smartfold	Source code
sortGenotypes	Man page Source code
split_genotype_cols	Source code
spouses	Man page Source code
stop2	Source code
stopifnot2	Source code
stopifnotSimpleVector	Source code
subnucs	Man page Source code
subset.ped	Man page Source code
summary.list	Source code
summary.ped	Source code
summary.singleton	Source code
swapSex	Man page Source code
tieLoops	Man page Source code
topolOrder	Source code
transferMarkers	Man page Source code
trioCheckFast	Source code
trivialMut	Source code
typedMembers	Man page Source code
unmaskPed	Man page Source code
unrelated	Man page Source code
untypedMembers	Man page Source code
validateMarker	Source code
validatePed	Man page Source code
validate_sex	Source code
whichMarkers	Man page Source code
writeFreqDatabase	Man page Source code
writeMerlin	Source code
writePed	Man page Source code
writePed_merlin	Source code