Parametric Linkage and Other Pedigree Analysis in R
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Documentation for package ‘paramlink’ version 1.1-5
Help Pages
A B C D E F G H I J K L M N O P Q R S T U W X
-- A --
| addDaughter | Modify the pedigree of 'linkdat' objects |
| addMarker | Marker functions |
| addOffspring | Modify the pedigree of 'linkdat' objects |
| addParents | Modify the pedigree of 'linkdat' objects |
| addSon | Modify the pedigree of 'linkdat' objects |
| allGenotypes | Genotype combinations |
| ancestors | Pedigree subsets |
| as.data.frame.linkdat | linkdat to data.frame conversion |
| as.data.frame.linkres | S3 methods for class 'linkres'. |
| as.matrix.linkdat | linkdat to matrix conversion |
-- B --
| branch | Modify the pedigree of 'linkdat' objects |
| breakLoops | Pedigree loops |
-- C --
| connectedComponents | Convert 'Familias' output to linkdat objects |
| cousinPed | Create simple pedigrees |
| cousins | Pedigree subsets |
| cousinsPed | Create simple pedigrees |
-- D --
| descendants | Pedigree subsets |
| dominant | Example pedigree for linkage analysis |
| doubleCousins | Create simple pedigrees |
| doubleFirstCousins | Create simple pedigrees |
-- E --
| examineKinships | Check pedigree for relationship errors |
| exclusionPower | Power of exclusion |
-- F --
| Familias2linkdat | Convert 'Familias' output to linkdat objects |
| fast.grid | Genotype combinations |
| findLoopBreakers | Pedigree loops |
| findLoopBreakers2 | Pedigree loops |
| fullSibMating | Create simple pedigrees |
-- G --
| geno.grid.subset | Genotype combinations |
| getMarkers | Marker functions |
| grandparents | Pedigree subsets |
-- H --
| halfCousinPed | Create simple pedigrees |
| halfCousinsPed | Create simple pedigrees |
| halfSibStack | Create simple pedigrees |
| hasCA | Pairwise common ancestors |
-- I --
| IBDestimate | Relatedness estimation |
| IBDtriangle | IBD triangle plot |
| inbreeding | Relatedness coefficients |
| is.linkdat | Is an object a linkdat object? |
| is.linkdat.list | Is an object a linkdat object? |
| is.singleton | Is an object a linkdat object? |
-- J --
| jacquard | Relatedness coefficients |
| jacquard2 | Relatedness coefficients |
-- K --
| kinship_coefs | Relatedness coefficients |
-- L --
| leaves | Pedigree subsets |
| likelihood | Pedigree likelihood |
| likelihood.linkdat | Pedigree likelihood |
| likelihood.list | Pedigree likelihood |
| likelihood.singleton | Pedigree likelihood |
| likelihood_LINKAGE | Pedigree likelihood |
| linkage.power | Power of a linkage study |
| linkageSim | Simulate markers linked to a disease locus. |
| linkdat | Linkdat objects |
| linkres | S3 methods for class 'linkres'. |
| lod | Two-point LOD score |
| lod.peaks | LOD score peaks |
| LR | Likelihood ratios of pedigree hypotheses |
-- M --
| marker | Marker functions |
| markers | Marker functions |
| markerSim | Marker simulation |
| mendelianCheck | Check for Mendelian errors |
| mergePed | Merge two pedigrees |
| merlin | MERLIN wrappers |
| merlinUnlikely | MERLIN wrappers |
| modifyMarker | Marker functions |
| modifyMarkerMatrix | Marker functions |
-- N --
| nephews_nieces | Pedigree subsets |
| nuclearPed | Create simple pedigrees |
-- O --
| offspring | Pedigree subsets |
| oneMarkerDistribution | Genotype probability distribution |
-- P --
| parents | Pedigree subsets |
| peakSummary | S3 methods for class 'linkres'. |
| pedCreate | Create simple pedigrees |
| pedigreeLoops | Pedigree loops |
| pedModify | Modify the pedigree of 'linkdat' objects |
| pedParts | Pedigree subsets |
| plot.linkdat | Plot pedigrees with genotypes |
| plot.linkres | S3 methods for class 'linkres'. |
| plot.singleton | Plot pedigrees with genotypes |
| plotPedList | Plot a list of pedigrees. |
| print.linkdat | Linkdat objects |
| print.linkdat.model | Set, change or display the model parameters for 'linkdat' objects |
| print.linkres | S3 methods for class 'linkres'. |
-- Q --
| quadHalfFirstCousins | Create simple pedigrees |
-- R --
| randomPed | Random pedigree |
| readDatfile | Read dat file in LINKAGE format |
| readFamiliasLoci | Convert 'Familias' output to linkdat objects |
| relabel | Modify the pedigree of 'linkdat' objects |
| related.pairs | Pedigree subsets |
| relatednessCoeff | Relatedness coefficients |
| relationLR | Relationship Likelihood Ratio |
| removeIndividuals | Modify the pedigree of 'linkdat' objects |
| removeMarkers | Marker functions |
| restore_linkdat | linkdat to matrix conversion |
-- S --
| setAvailable | Functions for modifying availability vectors |
| setMarkers | Marker functions |
| setModel | Set, change or display the model parameters for 'linkdat' objects |
| setPlotLabels | Attach plot labels to a linkdat object |
| showInTriangle | Add points to the IBD triangle |
| siblings | Pedigree subsets |
| simpleSim | Unconditional marker simulation |
| singleton | Linkdat objects |
| spouses | Pedigree subsets |
| subset.linkdat | Linkdat objects |
| summary.linkdat | Linkdat objects |
| summary.linkres | S3 methods for class 'linkres'. |
| summary.powres | Power of a linkage study |
| swapAff | Modify the pedigree of 'linkdat' objects |
| swapAvailable | Functions for modifying availability vectors |
| swapGenotypes | Marker functions |
| swapSex | Modify the pedigree of 'linkdat' objects |
-- T --
| tieLoops | Pedigree loops |
| toyped | Toy pedigree for linkage analysis |
| transferMarkerdata | Transfer marker data |
| trim | Modify the pedigree of 'linkdat' objects |
| twoloops | A consanguineous pedigree |
| twoMarkerDistribution | Genotype probability distribution |
-- U --
| unrelated | Pedigree subsets |
-- W --
| write.linkdat | Linkdat objects |
-- X --
| Xped | Example pedigree with X-linked disease pattern. |