Package: paramlink 1.1-5
Magnus Dehli Vigeland
paramlink: Parametric Linkage and Other Pedigree Analysis in R
NOTE: 'PARAMLINK' HAS BEEN SUPERSEDED BY THE 'PED SUITE' PACKAGES (<https://magnusdv.github.io/pedsuite/>). 'PARAMLINK' IS MAINTAINED ONLY FOR LEGACY PURPOSES AND SHOULD NOT BE USED IN NEW PROJECTS. 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).
Authors:
paramlink_1.1-5.tar.gz
paramlink_1.1-5.zip(r-4.5)paramlink_1.1-5.zip(r-4.4)paramlink_1.1-5.zip(r-4.3)
paramlink_1.1-5.tgz(r-4.4-any)paramlink_1.1-5.tgz(r-4.3-any)
paramlink_1.1-5.tar.gz(r-4.5-noble)paramlink_1.1-5.tar.gz(r-4.4-noble)
paramlink_1.1-5.tgz(r-4.4-emscripten)paramlink_1.1-5.tgz(r-4.3-emscripten)
paramlink.pdf |paramlink.html✨
paramlink/json (API)
NEWS
| # Install 'paramlink' in R: |
| install.packages('paramlink', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/magnusdv/paramlink/issues
Last updated 3 years agofrom:8f948b15bb. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 02 2024 |
| R-4.5-win | NOTE | Nov 02 2024 |
| R-4.5-linux | NOTE | Nov 02 2024 |
| R-4.4-win | OK | Nov 02 2024 |
| R-4.4-mac | OK | Nov 02 2024 |
| R-4.3-win | OK | Nov 02 2024 |
| R-4.3-mac | OK | Nov 02 2024 |
Exports:addDaughteraddMarkeraddOffspringaddParentsaddSonallGenotypesancestorsbranchbreakLoopsconnectedComponentscousinPedcousinscousinsPeddescendantsdoubleCousinsdoubleFirstCousinsexamineKinshipsexclusionPowerFamilias2linkdatfast.gridfindLoopBreakersfindLoopBreakers2fullSibMatinggeno.grid.subsetgetMarkersgrandparentshalfCousinPedhalfCousinsPedhalfSibStackhasCAIBDestimateIBDtriangleinbreedingis.linkdatis.linkdat.listis.singletonjacquardjacquard2kinship_coefsleaveslikelihoodlikelihood_LINKAGElinkage.powerlinkageSimlinkdatlodlod.peaksLRmarkermarkerSimmendelianCheckmergePedmerlinmerlinUnlikelymodifyMarkermodifyMarkerMatrixnephews_niecesnuclearPedoffspringoneMarkerDistributionparentspeakSummarypedigreeLoopsplotPedListquadHalfFirstCousinsrandomPedreadDatfilereadFamiliasLocirelabelrelated.pairsrelationLRremoveIndividualsremoveMarkersrestore_linkdatsetAvailablesetMarkerssetModelsetPlotLabelsshowInTrianglesiblingssimpleSimsingletonspousesswapAffswapAvailableswapGenotypesswapSextieLoopstransferMarkerdatatrimtwoMarkerDistributionunrelatedwrite.linkdat
Dependencies:assertthatdigestevaluategenericshighrkinship2knitrlatticeMatrixmaxLikmiscToolsquadprogsandwichxfunyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Genotype combinations | allGenotypes fast.grid geno.grid.subset |
| linkdat to data.frame conversion | as.data.frame.linkdat |
| linkdat to matrix conversion | as.matrix.linkdat restore_linkdat |
| Example pedigree for linkage analysis | dominant |
| Check pedigree for relationship errors | examineKinships |
| Power of exclusion | exclusionPower |
| Convert 'Familias' output to linkdat objects | connectedComponents Familias2linkdat readFamiliasLoci |
| Pairwise common ancestors | hasCA |
| Relatedness estimation | IBDestimate |
| IBD triangle plot | IBDtriangle |
| Is an object a linkdat object? | is.linkdat is.linkdat.list is.singleton |
| Pedigree likelihood | likelihood likelihood.linkdat likelihood.list likelihood.singleton likelihood_LINKAGE |
| Power of a linkage study | linkage.power summary.powres |
| Simulate markers linked to a disease locus. | linkageSim |
| Linkdat objects | linkdat print.linkdat singleton subset.linkdat summary.linkdat write.linkdat |
| S3 methods for class 'linkres'. | as.data.frame.linkres linkres peakSummary plot.linkres print.linkres summary.linkres |
| Two-point LOD score | lod |
| LOD score peaks | lod.peaks |
| Likelihood ratios of pedigree hypotheses | LR |
| Marker functions | addMarker getMarkers marker markers modifyMarker modifyMarkerMatrix removeMarkers setMarkers swapGenotypes |
| Marker simulation | markerSim |
| Check for Mendelian errors | mendelianCheck |
| Merge two pedigrees | mergePed |
| MERLIN wrappers | merlin merlinUnlikely |
| Genotype probability distribution | oneMarkerDistribution |
| Create simple pedigrees | cousinPed cousinsPed doubleCousins doubleFirstCousins fullSibMating halfCousinPed halfCousinsPed halfSibStack nuclearPed pedCreate quadHalfFirstCousins |
| Pedigree loops | breakLoops findLoopBreakers findLoopBreakers2 pedigreeLoops tieLoops |
| Modify the pedigree of 'linkdat' objects | addDaughter addOffspring addParents addSon branch pedModify relabel removeIndividuals swapAff swapSex trim |
| Pedigree subsets | ancestors cousins descendants grandparents leaves nephews_nieces offspring parents pedParts related.pairs siblings spouses unrelated |
| Plot pedigrees with genotypes | plot.linkdat plot.singleton |
| Plot a list of pedigrees. | plotPedList |
| Random pedigree | randomPed |
| Read dat file in LINKAGE format | readDatfile |
| Relatedness coefficients | inbreeding jacquard jacquard2 kinship_coefs relatednessCoeff |
| Relationship Likelihood Ratio | relationLR |
| Functions for modifying availability vectors | setAvailable swapAvailable |
| Set, change or display the model parameters for 'linkdat' objects | print.linkdat.model setModel |
| Attach plot labels to a linkdat object | setPlotLabels |
| Add points to the IBD triangle | showInTriangle |
| Unconditional marker simulation | simpleSim |
| Toy pedigree for linkage analysis | toyped |
| Transfer marker data | transferMarkerdata |
| A consanguineous pedigree | twoloops |
| Genotype probability distribution | twoMarkerDistribution |
| Example pedigree with X-linked disease pattern. | Xped |