findDiffExpressed: Finding differentially expressed genes.

In KonradZych/phenotypes2genotypes: High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains

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.

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.).

Value

Object of class population.

Author(s)

Konrad Zych [e-mail], Danny Arends [e-mail] Maintainer: Konrad Zych [e-mail]

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

	data(testPopulation)
	testPopulation <- find.diff.expressed(testPopulation)

KonradZych/phenotypes2genotypes documentation built on May 30, 2019, 2:45 p.m.