genomesim
(Package: pedantics) :
A function to simulate QTL and/or SNP data.
Simulates a chromosome of arbitrary length with arbitrary numbers, types, and spacings of genetic loci over arbitrary pedigrees.
● Data Source:
CranContrib
● Keywords: datagen
● Alias: genomesim
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rpederrBird
(Package: pedantics) :
Permutes a bird pedigree to create a plausible complete pedigree
Permutes a pedigree to create a plausible complete pedigree, with errors accounted for in terms of extra-pair paternity.
● Data Source:
CranContrib
● Keywords: datagen
● Alias: rpederrBird
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microsim
(Package: pedantics) :
Simulates microsatellite data across a pedigree.
Uses a pedgiree with parents identified for all non-founding individuas and simulates microsatellite genotypes
● Data Source:
CranContrib
● Keywords: datagen
● Alias: microsim
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phensim
(Package: pedantics) :
A function to simulated phenotypic data
Simulates phenotypic data across arbitrary pedigrees. phensim simulate direct, maternal and paternal genetica and environmental effects for an arbitrary number of traits with arbitrary patterns of missing data.
● Data Source:
CranContrib
● Keywords: datagen
● Alias: phensim
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rpederr
(Package: pedantics) :
Permutes a pedigree to create a plausible complete pedigree
Given estimates of indivdiual life histories and rates and patterns of errors in pedigree links, rpederr probabilistically assigns "true" parents given an incomplete and potentially eroneous pedigree.
● Data Source:
CranContrib
● Keywords: datagen
● Alias: rpederr
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pedigreeStats
(Package: pedantics) :
Calculates a range of statistics of pedigrees.
Statistics are those that will hopefully be useful for describing pedigrees to be used in quantitative genetic analyses of natural populations. This module will be most useful when cohort affinities for all individuals can be provided. All outputs are produced in a numerical form as well as in graphical summaries.
● Data Source:
CranContrib
● Keywords:
● Alias: pedigreeStats
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pedStatSummary
(Package: pedantics) :
Post-processes output from pedigreeStats
Generates a manageable summary of pedigree-wide statistics reported by pedigreeStats, either for a single pedigree or for a comparison between pedigrees
● Data Source:
CranContrib
● Keywords: manip
● Alias: pedStatSummary
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drawPedigree
(Package: pedantics) :
Produce a graphical representation of a pedigree
Plots a pedigree, with options specific to considerations for pedigrees used to for quantitative genetic inferencein natural populations. Pedigrees containing only those individuals that are informative with respect to (genetic) variation in an arbitrary trait can be plotted, potentially overlain on a complete pedigree. Functions also exist to plot various types of pedgiree links associated with focal individuals.
● Data Source:
CranContrib
● Keywords: hplot
● Alias: drawPedigree
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pedantix contains three types of functions. The first are functions specifically designed to aid power and sensitivity analyses for quantitative genetic studies, particulary with thought to accommodating the proglems and data structures that arise in data from natural populations. There are basic utility functions for manipulating pedigrees. Finally there are functions for visualizing and statistically characterizing pedigrees.
● Data Source:
CranContrib
● Keywords: package
● Alias: pedantics, pedantics-package
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fpederr
(Package: pedantics) :
Simulates a pedigree with errors and missing data from a complete pedigree.
Implements the 'forward' approach to producing pairs of pedigrees for power and sensitivity analyses.
● Data Source:
CranContrib
● Keywords: datagen
● Alias: fpederr
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