R: Initialize an experiment design matrix

initialDesign {designGG}

R Documentation

Initialize an experiment design matrix

Description

Allocate RILs (or strains) into different conditional and pair RILs (or strains) into slides.

Usage

  initialDesign( genotype, nRILs, nSlides, nConditions, nTuple, 
                 bTwoColorArray )

Arguments

`genotype`	genotype data: a nMarker-by-nRILs matrix with two allels being 0 and 1 (or A and B) or three allels being 0, 0.5 and 1 (or, A, H, and B), where 0.5 (or H) represents heterozygous allele.
`nRILs`	total number of RILs ((or strains) available for the experiment.
`nSlides`	total number of slides available for the experiment.
`nConditions`	number of all possible combination of all environmental factors.
`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 shw the message below, `warning: "The number of slides is too small to perform the experiment."`
`bTwoColorArray`	binary variable indicating experiment type: `bTwoColorArray <- T` #for dual channel experiment `bTwoColorArray <- F` #for single channel experiment

Details

For two-color array experiments, randomly choose a RIL (or strain) and pair it with the genetically most different RIL (or strain) on one array.
For one-color array experiments, array.allocation is NULL as there is no need to pair samples.

Value

a list with 2 matrices:
condition.allocation: allocate RILs (or strains) into different conditional (nCondition $times$ nRILs)
array.allocation: pair RILs (or strains) into sldies (nSlides $times$ nRILs)

Note

This function calls conditionAllocation function to allocate selected RILs (or strains) into different conditions.

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. (submitted)
http://gbic.biol.rug.nl/designGG

Examples

genotype <- read.table("genotype.txt")
nEnvFactors <- 2  
nLevels <- c( 2, 2 )
levels <- list ( c(16, 24), c(5, 10) )
nSlides <- 100
nTuple <- 25  
bTwoColorArray <- TRUE 
initialDesign( genotype, nRILs, nSlides, nConditions, nTuple, bTwoColorArray )

[Package designGG version 1.0-02 Index]