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.

Author
Magnus Dehli Vigeland
Date of publication
2016-10-17 00:37:57
Maintainer
Magnus Dehli Vigeland <magnusdv@studmed.uio.no>
License
GPL (>= 2)
Version
0.9-9

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
inbreeding
Inbreeding coefficients and Jacquard coefficients
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
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 analysis in R
plot.linkdat
Plot pedigrees with genotypes
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'...
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.

Files in this package

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