R: Parametric Linkage and Other Pedigree Analysis in R

# Parametric Linkage and Other Pedigree Analysis in R

## Documentation for package ‘paramlink’ version 1.1-6

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I J K L M N O P Q R S T U W X

## -- A --

addDaughter | Modify the pedigree of 'linkdat' objects
addMarker | Marker functions
addOffspring | Modify the pedigree of 'linkdat' objects
addParents | Modify the pedigree of 'linkdat' objects
addSon | Modify the pedigree of 'linkdat' objects
allGenotypes | Genotype combinations
ancestors | Pedigree subsets
as.data.frame.linkdat | linkdat to data.frame conversion
as.data.frame.linkres | S3 methods for class 'linkres'.
as.matrix.linkdat | linkdat to matrix conversion

## -- B --

branch | Modify the pedigree of 'linkdat' objects
breakLoops | Pedigree loops

## -- C --

connectedComponents | Convert 'Familias' output to linkdat objects
cousinPed | Create simple pedigrees
cousins | Pedigree subsets
cousinsPed | Create simple pedigrees

## -- D --

descendants | Pedigree subsets
dominant | Example pedigree for linkage analysis
doubleCousins | Create simple pedigrees
doubleFirstCousins | Create simple pedigrees

## -- E --

examineKinships | Check pedigree for relationship errors
exclusionPower | Power of exclusion

## -- F --

Familias2linkdat | Convert 'Familias' output to linkdat objects
fast.grid | Genotype combinations
findLoopBreakers | Pedigree loops
findLoopBreakers2 | Pedigree loops
fullSibMating | Create simple pedigrees

## -- G --

geno.grid.subset | Genotype combinations
getMarkers | Marker functions
grandparents | Pedigree subsets

## -- H --

halfCousinPed | Create simple pedigrees
halfCousinsPed | Create simple pedigrees
halfSibStack | Create simple pedigrees
hasCA | Pairwise common ancestors

## -- I --

IBDestimate | Relatedness estimation
IBDtriangle | IBD triangle plot
inbreeding | Relatedness coefficients
is.linkdat | Is an object a linkdat object?
is.linkdat.list | Is an object a linkdat object?
is.singleton | Is an object a linkdat object?

## -- J --

jacquard | Relatedness coefficients
jacquard2 | Relatedness coefficients

## -- K --

kinship_coefs | Relatedness coefficients

## -- L --

leaves | Pedigree subsets
likelihood | Pedigree likelihood
likelihood.linkdat | Pedigree likelihood
likelihood.list | Pedigree likelihood
likelihood.singleton | Pedigree likelihood
likelihood_LINKAGE | Pedigree likelihood
linkage.power | Power of a linkage study
linkageSim | Simulate markers linked to a disease locus.
linkdat | Linkdat objects
linkres | S3 methods for class 'linkres'.
lod | Two-point LOD score
lod.peaks | LOD score peaks
LR | Likelihood ratios of pedigree hypotheses

## -- M --

marker | Marker functions
markers | Marker functions
markerSim | Marker simulation
mendelianCheck | Check for Mendelian errors
mergePed | Merge two pedigrees
merlin | MERLIN wrappers
merlinUnlikely | MERLIN wrappers
modifyMarker | Marker functions
modifyMarkerMatrix | Marker functions

## -- N --

nephews_nieces | Pedigree subsets
nuclearPed | Create simple pedigrees

## -- O --

offspring | Pedigree subsets
oneMarkerDistribution | Genotype probability distribution

## -- P --

parents | Pedigree subsets
peakSummary | S3 methods for class 'linkres'.
pedCreate | Create simple pedigrees
pedigreeLoops | Pedigree loops
pedModify | Modify the pedigree of 'linkdat' objects
pedParts | Pedigree subsets
plot.linkdat | Plot pedigrees with genotypes
plot.linkres | S3 methods for class 'linkres'.
plot.singleton | Plot pedigrees with genotypes
plotPedList | Plot a list of pedigrees.
print.linkdat | Linkdat objects
print.linkdat.model | Set, change or display the model parameters for 'linkdat' objects
print.linkres | S3 methods for class 'linkres'.

## -- Q --

quadHalfFirstCousins | Create simple pedigrees

## -- R --

randomPed | Random pedigree
readDatfile | Read dat file in LINKAGE format
readFamiliasLoci | Convert 'Familias' output to linkdat objects
relabel | Modify the pedigree of 'linkdat' objects
related.pairs | Pedigree subsets
relatednessCoeff | Relatedness coefficients
relationLR | Relationship Likelihood Ratio
removeIndividuals | Modify the pedigree of 'linkdat' objects
removeMarkers | Marker functions
restore_linkdat | linkdat to matrix conversion

## -- S --

setAvailable | Functions for modifying availability vectors
setMarkers | Marker functions
setModel | Set, change or display the model parameters for 'linkdat' objects
setPlotLabels | Attach plot labels to a linkdat object
showInTriangle | Add points to the IBD triangle
siblings | Pedigree subsets
simpleSim | Unconditional marker simulation
singleton | Linkdat objects
spouses | Pedigree subsets
subset.linkdat | Linkdat objects
summary.linkdat | Linkdat objects
summary.linkres | S3 methods for class 'linkres'.
summary.powres | Power of a linkage study
swapAff | Modify the pedigree of 'linkdat' objects
swapAvailable | Functions for modifying availability vectors
swapGenotypes | Marker functions
swapSex | Modify the pedigree of 'linkdat' objects

## -- T --

tieLoops | Pedigree loops
toyped | Toy pedigree for linkage analysis
transferMarkerdata | Transfer marker data
trim | Modify the pedigree of 'linkdat' objects
twoloops | A consanguineous pedigree
twoMarkerDistribution | Genotype probability distribution

## -- U --

unrelated | Pedigree subsets

## -- W --

write.linkdat | Linkdat objects

## -- X --

Xped | Example pedigree with X-linked disease pattern.