variableNames: Generate variable names for all factors
In designGG: Computational tool for designing genetical genomics experiments.

Description Usage Arguments Details Value Author(s) References See Also

Generate variable names for genetic, environmental factors and interacting terms.

1	variableNames(nEnvFactors, envFactorNames=NULL)

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.

envFactorNames

a vector with names for all environmental factor(s). For example, for the 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.

generates names for variables, a vector with the length of (variableNumber+1).

When nEnvFactors = 1 and nLevels = 1, there is no environmetal pertubation in the experimental. Then we re-define nEnvFactors to be 0 within the algorithm. Accordingly, variableNumber = 1, and variableNames is one genetic factor "Q".
When nEnvFactors = 1, variableNumber = 3, and variableNames are one genetic factor "Q", one environmental factor "F", and one interacting factor "QxF".
When nEnvFactors = 2, variableNumber = 7, and variableNames are one genetic factor "Q", two environmental factors "F1" and "F2", three two-way interacting factors "QF1", "QF2", "F1F2", and one three way interacting factors "QxF1xF2".
When nEnvFactors = 3, variableNumber = 15, and variableNames are one genetic factor "Q", three environmental factors "F1", "F2" and "F3", six two-way interacting factors "QF1", "QF2", "QF3", "F1F2", "F2F3" and "F1F3", four three-way interacting factors "QxF1xF2", "QxF1xF3", "QxF2xF3", "F1xF2xF3" and one four-way interacting factors "QxF1xF2xF3".

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>

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

variableNumber

designGG documentation built on May 2, 2019, 5:51 a.m.