pheno2geno (version 1.4.0)

find.diff.expressed: Finding differentially expressed genes.

Description

Using Rank Product or student t-test analysis to select differentially expressed genes.

Usage

find.diff.expressed(population,use=c("ttest","rankprod"),verbose=FALSE,
  debugMode=0,...)

Arguments

population

An object of class population. See create.population for details.

use

Which method should be used for selecting differentially expressed probes:

• ttest - student t-test.

• rankprod - Rank Product using RP function from RankProd package. RankProd package from Bioconductor has to be installed before this option is enabled.

verbose

Be verbose.

debugMode

1: Print out checks, 2: print additional time information.

...

Additional arguments passed to RP function.

Value

Object of class population.

Details

This function finds probes differentially expressed between founders using either student t.test or RankProd (RankProd package from Bioconductor has to be installed before this option is enabled.).

References

Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J.(2006) RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics, 15;22(22):2825-7.

See Also

• RP - Perform rank product method to identify differentially expressed genes.

• read.population - Load genotype, phenotype, genetic map data files into R environment into a population object.

• generate.biomarkers - Creating genotypes from children phenotypes.

• showRPpval- Printing out p-values calculated by the find.diff.expressed function.

• plotRPpval - Plotting p-values calculated by the find.diff.expressed function.

Examples

# NOT RUN {
	data(testPopulation)
	testPopulation <- find.diff.expressed(testPopulation)

# }