Computational tool for designing genetical genomics experiments.

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Documentation for package ‘designGG’ version 1.1

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acceptanceProbability Compute the acceptance probability for each updated design
arrayUpdate Update array allocation
conditionAllocation Allocate the selected RILs into different conditions
conditionCombination Generate a matrix indicating all possible levels for environmental factors
conditionLevel Levels of all environmental factors
conditionUpdate Update condition allocation
design genetical genomics experiment Optimal design for genetical genomics experiments
designGG Optimal design for genetical genomics experiments
designScore Calculate the A- or D- optimality score based on current experimental design
exampleArrayDesignTable Example output of ArrayDesignTable data
exampleConditionDesignTable Example ConditionDesignTable data
examplePlotObj Example PlotObj data
experimentDesignTable Make experiment table based design matrix
genotype Example genotype data
initialDesign Initialize an experiment design matrix
interactionLevel Generate levels for all interacting factors
pairLevel Pair levels for paired RILs (or strains)
plotAllScores Plot scores profiles
temperatureStep Calculate the temperature decreasing step for simulated annealing process
updateDesign Updates current design
variableNames Generate variable names for all factors
variableNumber Compute the number of variables in the experiment