paramlink: Parametric Linkage and Other Pedigree Analysis in R

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).

AuthorMagnus Dehli Vigeland
Date of publication2017-03-13 13:18:35
MaintainerMagnus Dehli Vigeland <magnusdv@studmed.uio.no>
LicenseGPL (>= 2)
Version1.1-0

View on CRAN

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

addDaughter Man page
addMarker Man page
addOffspring Man page
addParents Man page
addSon Man page
all.equal.linkdat Man page
allGenotypes Man page
ancestors Man page
as.data.frame.linkdat Man page
as.data.frame.linkres Man page
as.matrix.linkdat Man page
branch Man page
breakLoops Man page
connectedComponents Man page
cousinPed Man page
cousins Man page
cousinsPed Man page
createPedigree Man page
descendants Man page
dominant Man page
doubleCousins Man page
doubleFirstCousins Man page
examineKinships Man page
exclusionPower Man page
Familias2linkdat Man page
fast.grid Man page
findLoopBreakers Man page
findLoopBreakers2 Man page
fullSibMating Man page
geno.grid.subset Man page
getMarkers Man page
grandparents Man page
halfCousinPed Man page
halfCousinsPed Man page
halfSibStack Man page
IBDestimate Man page
IBDtriangle Man page
inbreeding Man page
is.linkdat Man page
is.linkdat.list Man page
is.singleton Man page
jacquard Man page
jacquard2 Man page
kinship.coeff Man page
leaves Man page
likelihood Man page
likelihood_LINKAGE Man page
likelihood.linkdat Man page
likelihood.list Man page
likelihood.singleton Man page
linkage.power Man page
linkageSim Man page
linkdat Man page
linkdat.utils Man page
linkres Man page
lod Man page
lod.peaks Man page
marker Man page
markerSim Man page
mendelianCheck Man page
mergePed Man page
merlin Man page
merlinUnlikely Man page
modifyMarker Man page
modifyMarkerMatrix Man page
modifyPedigree Man page
nephews_nieces Man page
nuclearPed Man page
offspring Man page
oneMarkerDistribution Man page
paramlink Man page
paramlink-package Man page
parents Man page
peakSummary Man page
pedigreeLoops Man page
plot.linkdat Man page
plot.linkres Man page
plotPedList Man page
plot.singleton Man page
power.varyPar Man page
print.linkdat Man page
print.linkdat.model Man page
print.linkres Man page
quadHalfFirstCousins Man page
randomPed Man page
readDatfile Man page
relabel Man page
related.pairs Man page
relationLR Man page
removeIndividuals Man page
removeMarkers Man page
restore_linkdat Man page
setAvailable Man page
setMap Man page
setMarkers Man page
setModel Man page
setPlotLabels Man page
siblings Man page
simpleSim Man page
singleton Man page
spouses Man page
subset.linkdat Man page
summary.linkdat Man page
summary.linkres Man page
summary.powres Man page
swapAff Man page
swapAvailable Man page
swapGenotypes Man page
swapSex Man page
tieLoops Man page
toyped Man page
transferMarkerdata Man page
trim Man page
twoloops Man page
twoMarkerDistribution Man page
unrelated Man page
write.linkdat Man page
Xped Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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