R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
CranContrib
BioConductor
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Results 1 - 10 of 30 found.
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modifyPedigree (Package: paramlink) : Modify the pedigree of 'linkdat' objects

Functions to modify the pedigree of a 'linkdat' object.

● Data Source: CranContrib
● Keywords: manip
● Alias: addDaughter, addOffspring, addParents, addSon, branch, modifyPedigree, relabel, removeIndividuals, swapAff, swapSex, trim
● 0 images

linkageSim (Package: paramlink) :

Simulates markers (with up to 4 alleles) conditional on the pedigree structure, affection statuses and disease model.

● Data Source: CranContrib
● Keywords: datagen
● Alias: linkageSim
● 0 images

markers (Package: paramlink) :

Functions for setting and manipulating marker genotypes for 'linkdat' objects.

● Data Source: CranContrib
● Keywords: manip
● Alias: addMarker, getMarkers, marker, mendelianCheck, modifyMarker, modifyMarkerMatrix, removeMarkers, setMap, setMarkers, swapGenotypes
● 0 images

allGenotypes (Package: paramlink) :

Auxiliary functions computing possible genotype combinations in a pedigree. These are not normally intended for end users.

● Data Source: CranContrib
● Keywords: methods
● Alias: allGenotypes, fast.grid, geno.grid.subset
● 0 images

plot.linkdat (Package: paramlink) :

This is the main function for pedigree plotting, with many options for controlling the appearance of pedigree symbols, labels and marker genotypes. Most of the work is done by the plotting functionality in the 'kinship2' package.

● Data Source: CranContrib
● Keywords: plot
● Alias: plot.linkdat, plot.singleton
● 0 images

markerSim (Package: paramlink) :

Simulates marker genotypes conditional on the pedigree structure, affection statuses and disease model.

● Data Source: CranContrib
● Keywords: datagen
● Alias: markerSim
● 0 images

likelihood (Package: paramlink) : Pedigree likelihood

Calculates various forms of pedigree likelihoods.

● Data Source: CranContrib
● Keywords: math
● Alias: likelihood, likelihood.linkdat, likelihood.list, likelihood.singleton, likelihood_LINKAGE
● 0 images

merlin (Package: paramlink) :

These functions require MERLIN to be installed and correctly pointed to in the PATH environment variable. The required input files are automatically created (in the working directory) and deleted afterwards. The MERLIN command is executed via a call to system().

● Data Source: CranContrib
● Keywords: manip
● Alias: merlin, merlinUnlikely
● 0 images

examineKinships (Package: paramlink) :

The function IBDestimate estimates IBD coefficients (k0, k1, k2) for specified pairs of pedigree members, using maximum likelihood methods (imported from the maxLik package).

● Data Source: CranContrib
● Keywords: math
● Alias: IBDestimate, examineKinships
● 0 images

inbreeding (Package: paramlink) :

Computes inbreeding coefficients for all pedigree members.

● Data Source: CranContrib
● Keywords: math
● Alias: inbreeding
● 0 images