conditionCombination {designGG}R Documentation

Generate a matrix indicating all possible levels for environmental factors

Description

Generate a matrix indicating all possible levels for environmental factors with dimension nConditions * nEnvFactors. This is a subfunction needed for designScore, but is not directly used.

Usage

  conditionCombination( nEnvFactors, nLevels, Level, envFactorNames )

Arguments

nEnvFactors

number of environmental factors, an integer bewteen 1 and 3. When nEnvFactors is 1 and the number of levels for the enviromental factor (nLevels) is 1, there is one condition in the experiment (i.e. no enviromental perturbation) and thus only genetic factor will be considered in the algorithm. When nEnvFactors is 1 and nLevels is larger than 1 or nEnvFactors is larger than 1, all main factor(s) and interacting facotr(s) will be included. Examples: If there is a temperature perturbation, then nEnvFactors is 1; If there is both temperature and drug treatment perturbation, then nEnvFactors is 2.

nLevels

number of levels for each factor, a vector with each component being integer. The length should be equal to nEnvFactors.

Level

a list which specifies the levels for each factor in the experiment. There are in total nEnvFactors elements in the list and each element correspsonds to certain envrironmental factor. The element is a vector describing all levels of the environmental factor. Default setting for the level of each factor is 1, 2, ...., nLevels[i]. (Here nLevels[i] is the ith element of nLevels, which tells the total number of levels for i environmental factor).

envFactorNames

a vector with names for all environmental factor(s). For example, for an experiment with two environmental factors of temperature and drug treatment: envFactorNames <- c( "Temperature", "Dosage" )
Default = NULL, then the output will use "F1" and "F2" to indicate the environmental factors.

Details

Currently this function works only when nEnvFactors is between 1 and 3.

Value

A matrix with dimension of nConditions * nEnvFactors. Each element in the matrix indicates the levels of corresponding environmental factor.

Author(s)

Yang Li <yang.li@rug.nl>, Gonzalo Vera <gonzalo.vera.rodriguez@gmail.com>
Rainer Breitling <r.breitling@rug.nl>, Ritsert Jansen <r.c.jansen@rug.nl>

References

Y. Li, R. Breitling and R.C. Jansen. Generalizing genetical genomics: the added value from environmental perturbation, Trends Genet (2008) 24:518-524.
Y. Li, M. Swertz, G. Vera, J. Fu, R. Breitling, and R.C. Jansen. designGG: An R-package and Web tool for the optimal design of genetical genomics experiments. BMC Bioinformatics 10:188(2009)
http://gbic.biol.rug.nl/designGG

See Also

designScore


[Package designGG version 1.1 Index]