updateDesign {designGG}R Documentation

Updates current design

Description

Updates current experimental design (including array.allocation and condition.allocation).

Usage

  updateDesign( array.allocation, condition.allocation, nRILs, 
                nSlides, nEnvFactors, nTuple, bTwoColorArray )

Arguments

array.allocation

matrix with nArray rows and nRIL columns. Elements of 1/0 indicate this RIL (or strain) is/not selected for this array.

condition.allocation

matrix with nCondition rows and nRIL columns. Elements of 1/0 indicate this RIL (or strain) is/not selected for this condition.

nRILs

number of RILs (or strains) available for the experiment.

nSlides

total number of slides available for experiment.

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.

nTuple

average number of RILs (or strains) to be assigned onto each condition.
nTuple should be a real number which is larger than 1.
If nTuple < 1, the algorithm will stop and show the message,
warning: "The number of slides is too small to perform the experiment."

bTwoColorArray

binary variable indicating experiment type:
bTwoColorArray <- TRUE \#for dual channel experiment
bTwoColorArray <- FALSE \#for single channel experiment

Details

This function calls two subfunctions: conditionUpdate and arrayUpdate.

Value

a list with two elements, array.allocation and condition.allocation.

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


[Package designGG version 1.1 Index]