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designGG (version 1.1)
Computational tool for designing genetical genomics experiments.
Description
The package provides R scripts for designing genetical genomics experiments.
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Version
Version
1.1
Install
install.packages('designGG')
Monthly Downloads
17
Version
1.1
License
GPL
Maintainer
Yang Li
Last Published
February 19th, 2013
Functions in designGG (1.1)
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examplePlotObj
Example PlotObj data
interactionLevel
Generate levels for all interacting factors
pairLevel
Pair levels for paired RILs (or strains)
acceptanceProbability
Compute the acceptance probability for each updated design
updateDesign
Updates current design
variableNumber
Compute the number of variables in the experiment
conditionLevel
Levels of all environmental factors
arrayUpdate
Update array allocation
plotAllScores
Plot scores profiles
temperatureStep
Calculate the temperature decreasing step for simulated annealing process
conditionAllocation
Allocate the selected RILs into different conditions
conditionUpdate
Update condition allocation
genotype
Example genotype data
designGG
Optimal design for genetical genomics experiments
variableNames
Generate variable names for all factors
initialDesign
Initialize an experiment design matrix
conditionCombination
Generate a matrix indicating all possible levels for environmental factors
exampleConditionDesignTable
Example ConditionDesignTable data
experimentDesignTable
Make experiment table based design matrix
designScore
Calculate the A- or D- optimality score based on current experimental design
exampleArrayDesignTable
Example output of ArrayDesignTable data