paramlink: Parametric Linkage Analysis in R

Parametric linkage analysis and other likelihood-based pedigree analyses based on the Elston-Stewart algorithm, including singlepoint LOD scores, power analysis and computation of marker genotype distributions. Multipoint analysis is provided through a convenient MERLIN wrapper. Includes many utility functions for creating, manipulating and plotting pedigrees, markers and linkage results.

AuthorMagnus Dehli Vigeland
Date of publication2016-10-17 00:37:57
MaintainerMagnus Dehli Vigeland <magnusdv@studmed.uio.no>
LicenseGPL (>= 2)
Version0.9-9

View on CRAN

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
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
fast.grid 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
inbreeding Man page
jacquard 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
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
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
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/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/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/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/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/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/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/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

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