Allocate the selected RILs into different conditions

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Description

This is a subfunction used by initialDesign but is not directly used. In the experiment where samples are profiled in pairs, the samples are firstly selected and paired on each array and then the selected samples are randomly allocated into different conditions.

Usage

1
  conditionAllocation( selectedRILs, genotype, nConditions, nSlides, nTuple )

Arguments

selectedRILs

the index of the selected RILs or strains among all that are available for the experiment.

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.

nConditions

number of all possible combination of all environmental factors. It should be larger than 1.

nSlides

total number of slides available for the experiment. It should be a non-zero integer.

nTuple

average number of RILs 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 a message as below,
warning: "The number of slides is too small to perform the experiment."

Details

This function is only called by initialDesign function when btwoColorArray is TRUE.

Value

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

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

initialDesign