paramlink: Parametric Linkage and Other Pedigree Analysis in R
Version 1.1-0

A suite of tools for analysing pedigrees with marker data, including parametric linkage analysis, forensic computations, relatedness analysis and marker simulations. The core of the package is an implementation of the Elston-Stewart algorithm for pedigree likelihoods, extended to allow mutations as well as complex inbreeding. Features for linkage analysis include singlepoint LOD scores, power analysis, and multipoint analysis (the latter through a wrapper to the MERLIN software). Forensic applications include exclusion probabilities, genotype distributions and conditional simulations. Data from the Familias software can be imported and analysed in paramlink. Finally, paramlink offers many utility functions for creating, manipulating and plotting pedigrees with or without marker data (the actual plotting is done by the kinship2 package).

Browse man pages Browse package API and functions Browse package files

AuthorMagnus Dehli Vigeland
Date of publication2017-03-13 13:18:35
MaintainerMagnus Dehli Vigeland <magnusdv@studmed.uio.no>
LicenseGPL (>= 2)
Version1.1-0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("paramlink")

Man pages

allGenotypes: Genotype combinations
as.data.frame.linkdat: linkdat to data.frame conversion
as.matrix.linkdat: linkdat to matrix conversion
createPedigree: Create simple pedigrees
dominant: Example pedigree for linkage analysis: 23 individuals, 650...
examineKinships: Relatedness estimation
exclusionPower: Power of exclusion
Familias2linkdat: Convert 'Familias' output to linkdat objects
IBDtriangle: IBD triangle plot
inbreeding: Inbreeding coefficients and Jacquard coefficients
is.linkdat: Is an object a linkdat object?
likelihood: Pedigree likelihood
linkage.power: Power of a linkage study
linkageSim: Simulate markers linked to a disease locus.
linkdat: linkdat objects
linkdat.utils: linkdat utilities
linkres: S3 methods for class 'linkres'.
lod: Two-point LOD score
lod.peaks: LOD score peaks
loops: Pedigree loops
markers: Marker functions
markerSim: Marker simulation
mergePed: Merge two pedigrees
merlin: MERLIN wrappers
modify: Modify the pedigree of 'linkdat' objects
oneMarkerDistribution: Genotype probability distribution
paramlink-package: Parametric Linkage and Other Pedigree Analysis in R
plot.linkdat: Plot pedigrees with genotypes
plotPedList: Plot a list of pedigrees.
randomPed: Random pedigree
readDatfile: Read dat file in LINKAGE format
relationLR: Relationship Likelihood Ratio
setAvailable: Functions for modifying availability vectors
setModel: Set, change or display the model parameters for 'linkdat'...
setPlotLabels: Attach plot labels to a linkdat object
simpleSim: Unconditional marker simulation
toyped: Toy pedigree for linkage analysis
twoloops: A consanguineous pedigree
twoMarkerDistribution: Genotype probability distribution
Xped: Example pedigree with X-linked disease pattern.

Functions

Familias2linkdat Man page Source code
IBDestimate Man page Source code
IBDsuspects Source code
IBDtriangle Man page Source code
SNPfreq Source code
SNPsim Source code
TRmatr Source code
TRmatrNEW 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 Man page 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.kinship2_pedigree Source code
as.matrix.linkdat Man page Source code
bdPrep Source code
bd_estim Source code
branch Man page Source code
breakLoops Man page Source code
build_genolist Source code
build_genolist_X Source code
checkMutationMatrix Source code
checkped Source code
comb2 Source code
connectedComponents Man page Source code
cousinPed Man page Source code
cousins Man page Source code
cousinsPed Man page Source code
createMarkerObject Source code
createPedigree Man page
descendants Man page Source code
descentPaths Source code
diallel2geno Source code
diallel2genoNEW Source code
dominant Man page
doubleCousins Man page Source code
doubleFirstCousins Man page Source code
eliminate Source code
eliminate_X Source code
errorModel 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
generations Source code
geno.grid.subset Man page Source code
geno2diallel Source code
geno2diallelNEW Source code
getMap Source code
getMarkers Man page Source code
getSex Source code
grandparents Man page Source code
halfCousinPed Man page Source code
halfCousinsPed Man page Source code
halfSibStack Man page Source code
haplonames 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.coeff 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
likelihoodSNP Source code
likelihood_LINKAGE Man page Source code
linkage.power Man page Source code
linkageSim Man page Source code
linkdat Man page Source code
linkdat.utils Man page
linkres Man page
lod Man page Source code
lod.peaks Man page Source code
lod.varyParam Source code
lodm Source code
make_arrays Source code
marker Man page Source code
markerSim Man page Source code
mendelianCheck Man page Source code
merge.linkdat 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
modifyPedigree Man page
myintersect Source code
mysetdiff Source code
nephews_nieces Man page Source code
nformative Source code
nitialCalc Source code
nternalID Source code
nuclearPed Man page Source code
offspring Man page Source code
oneMarkerDistribution Man page Source code
optimal.precomputation Source code
paramlink Man page
paramlink-package Man page
parents Man page Source code
peakSummary Man page Source code
pedigreeLoops Man page Source code
pedorder.parents.first Source code
peelFAST Source code
peelSNP Source code
peel_M Source code
peel_MD Source code
peel_MM 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 Man page Source code
prettyMarkers Source code
prettycat 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
rand01 Source code
randomPed Man page Source code
readDatfile Man page Source code
readMap Source code
reduce_alleles Source code
relabel Man page Source code
related.pairs Man page Source code
relationLR Man page Source code
removeIndividuals Man page Source code
removeMarkers Man page Source code
restore_linkdat Man page Source code
s.natural Source code
s.natural0 Source code
setAvailable Man page Source code
setMap Man page Source code
setMarkers Man page Source code
setModel Man page Source code
setPlotLabels Man page Source code
setSNPfreqs Source code
siblings Man page Source code
simpleSim Man page Source code
singleton Man page Source code
spouses Man page Source code
startdata_M Source code
startdata_MD Source code
startdata_MM 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
transferMarkerdataSingle 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

Files

NAMESPACE
NEWS
data
data/twoloops.rda
data/Xped.rda
data/dominant.rda
data/toyped.rda
R
R/modify.R
R/linkres.R
R/twoMarkerDistribution.R
R/utils.R
R/oneMarkerDistribution.R
R/loops.R
R/subset.linkdat.R
R/linkage.power.R
R/likelihood_LINKAGE.R
R/plot.linkdat.R
R/SNPsim.R
R/as.data.frame.linkdat.R
R/familias2linkdat.R
R/markers.R
R/markerSim.R
R/merlin.R
R/likelihoodSNP.R
R/as.matrix.linkdat.R
R/print.linkdat.R
R/plotPedList.R
R/setModel.R
R/relationLR.R
R/setMap.R
R/randomPed.R
R/likelihood.R
R/linkdat.R
R/createPedigree.R
R/linkageSim.R
R/write.linkdat.R
R/lod.R
R/exclusionPower.R
R/examineKinships.R
MD5
DESCRIPTION
man
man/IBDtriangle.Rd
man/modify.Rd
man/linkageSim.Rd
man/markers.Rd
man/allGenotypes.Rd
man/plot.linkdat.Rd
man/markerSim.Rd
man/likelihood.Rd
man/merlin.Rd
man/Familias2linkdat.Rd
man/examineKinships.Rd
man/inbreeding.Rd
man/relationLR.Rd
man/oneMarkerDistribution.Rd
man/lod.Rd
man/setModel.Rd
man/paramlink-package.Rd
man/mergePed.Rd
man/randomPed.Rd
man/createPedigree.Rd
man/dominant.Rd
man/lod.peaks.Rd
man/setPlotLabels.Rd
man/setAvailable.Rd
man/linkres.Rd
man/as.data.frame.linkdat.Rd
man/linkdat.utils.Rd
man/twoMarkerDistribution.Rd
man/readDatfile.Rd
man/loops.Rd
man/plotPedList.Rd
man/exclusionPower.Rd
man/as.matrix.linkdat.Rd
man/linkdat.Rd
man/twoloops.Rd
man/Xped.Rd
man/toyped.Rd
man/linkage.power.Rd
man/simpleSim.Rd
man/is.linkdat.Rd
paramlink documentation built on May 19, 2017, 3:42 p.m.