API for paramlink
Parametric Linkage and Other Pedigree Analysis in R

Global functions
.IBDlikelihood	Source code
.IBDsuspects	Source code
.SNPfreq	Source code
.SNPsim	Source code
.TRmatr	Source code
.TRmatrNEW	Source code
.as.kinship2_pedigree	Source code
.build_genolist	Source code
.build_genolist_X	Source code
.checkMutationMatrix	Source code
.check_parents_before_children	Source code
.checkped	Source code
.comb2	Source code
.createMarkerObject	Source code
.descentPaths	Source code
.diallel2geno	Source code
.diallel2genoNEW	Source code
.eliminate	Source code
.eliminate_X	Source code
.generations	Source code
.geno2diallel	Source code
.geno2diallelNEW	Source code
.getMap	Source code
.getSex	Source code
.haplonames	Source code
.informative	Source code
.initialCalc	Source code
.internalID	Source code
.is.natural	Source code
.is.natural0	Source code
.likelihoodSNP	Source code
.lod.varyParam	Source code
.lodm	Source code
.merge.linkdat	Source code
.myintersect	Source code
.mysetdiff	Source code
.onAttach	Source code
.optimal.precomputation	Source code
.peelFAST	Source code
.peelSNP	Source code
.peel_M	Source code
.peel_MD	Source code
.peel_MM	Source code
.prettyMarkers	Source code
.prettycat	Source code
.rand01	Source code
.readMap	Source code
.reduce_alleles	Source code
.reorder_parents_before_children	Source code
.setMap	Source code
.setSNPfreqs	Source code
.startdata_M	Source code
.startdata_MD	Source code
.startdata_MM	Source code
.transferMarkerdataSingle	Source code
Familias2linkdat	Man page Source code
IBDest_getAlleleData	Source code
IBDestimate	Man page Source code
IBDtriangle	Man page Source code
LR	Man page Source code
Xped	Man page
addDaughter	Man page Source code
addMarker	Man page Source code
addOffspring	Man page Source code
addParents	Man page Source code
addSon	Man page Source code
all.equal.linkdat	Source code
allGenotypes	Man page Source code
ancestors	Man page Source code
as.data.frame.linkdat	Man page Source code
as.data.frame.linkres	Man page Source code
as.matrix.linkdat	Man page Source code
branch	Man page Source code
breakLoops	Man page Source code
connectedComponents	Man page Source code
cousinPed	Man page Source code
cousins	Man page Source code
cousinsPed	Man page Source code
descendants	Man page Source code
dominant	Man page
doubleCousins	Man page Source code
doubleFirstCousins	Man page Source code
examineKinships	Man page Source code
exclusionPower	Man page Source code
fast.grid	Man page Source code
findLoopBreakers	Man page Source code
findLoopBreakers2	Man page Source code
fullSibMating	Man page Source code
geno.grid.subset	Man page Source code
getMarkers	Man page Source code
grandparents	Man page Source code
halfCousinPed	Man page Source code
halfCousinsPed	Man page Source code
halfSibStack	Man page Source code
hasCA	Man page Source code
inbreeding	Man page Source code
is.linkdat	Man page Source code
is.linkdat.list	Man page Source code
is.singleton	Man page Source code
jacquard	Man page Source code
jacquard2	Man page Source code
kinship_coefs	Man page Source code
leaves	Man page Source code
likelihood	Man page Source code
likelihood.linkdat	Man page Source code
likelihood.list	Man page Source code
likelihood.singleton	Man page Source code
likelihood_LINKAGE	Man page Source code
linkage.power	Man page Source code
linkageSim	Man page Source code
linkdat	Man page Source code
linkres	Man page
lod	Man page Source code
lod.peaks	Man page Source code
marker	Man page Source code
markerSim	Man page Source code
markers	Man page
mendelianCheck	Man page Source code
mergePed	Man page Source code
merlin	Man page Source code
merlinUnlikely	Man page Source code
modifyMarker	Man page Source code
modifyMarkerMatrix	Man page Source code
nephews_nieces	Man page Source code
nuclearPed	Man page Source code
offspring	Man page Source code
oneMarkerDistribution	Man page Source code
paramlink	Man page
paramlink-package	Man page
parents	Man page Source code
peakSummary	Man page Source code
pedCreate	Man page
pedModify	Man page
pedParts	Man page
pedigreeLoops	Man page Source code
pedlistMembership	Source code
plot.linkdat	Man page Source code
plot.linkres	Man page Source code
plot.singleton	Man page Source code
plotPedList	Man page Source code
power.varyPar	Source code
print.linkdat	Man page Source code
print.linkdat.model	Man page Source code
print.linkres	Man page Source code
quadHalfFirstCousins	Man page Source code
randomPed	Man page Source code
readDatfile	Man page Source code
readFamiliasLoci	Man page Source code
relabel	Man page Source code
related.pairs	Man page Source code
relatednessCoeff	Man page
relationLR	Man page Source code
removeIndividuals	Man page Source code
removeMarkers	Man page Source code
restore_linkdat	Man page Source code
setAvailable	Man page Source code
setMarkers	Man page Source code
setModel	Man page Source code
setPlotLabels	Man page Source code
showInTriangle	Man page Source code
siblings	Man page Source code
simpleSim	Man page Source code
singleton	Man page Source code
spouses	Man page Source code
subset.linkdat	Man page Source code
summary.linkdat	Man page Source code
summary.linkres	Man page Source code
summary.powres	Man page Source code
swapAff	Man page Source code
swapAvailable	Man page Source code
swapGenotypes	Man page Source code
swapSex	Man page Source code
tieLoops	Man page Source code
toyped	Man page
transferMarkerdata	Man page Source code
trim	Man page Source code
twoMarkerDistribution	Man page Source code
twoloops	Man page
unrelated	Man page Source code
write.linkdat	Man page Source code