GeneAnswers (version 2.14.0)

GeneAnswers-package: Integrated Interpretation of Genes

Description

GeneAnswers provide an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test.

Details

Package:

GeneAnswers

Type:

Package

Version:

1.6.0

Date:

2010-10-14

License:

LGPL version 2 or newer

References

1. Feng G, Shaw P, Rosen ST, Lin SM and Kibbe WA, 'Using the Bioconductor GeneAnswers Package to Interpret Gene Lists.' Methods Mol Biol. 2012 802:101-12.

2. Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10

3. Du, P., Feng, G., Flatow, J., Song, J., Holko, M., Kibbe, W.A. and Lin, S.M., (2009) 'From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations', Bioinformatics 25(12):i63-8

4. Osborne, J.D., Flatow, J., Holko, M., Lin, S.M., Kibbe, W.A., Zhu, L.J., Danila, M.I., Feng, G. and Chisholm, R.L., Annotating the human genome with Disease Ontology. BMC Genomics. 2009 Jul 7;10 Suppl 1:S6.

Examples

data('humanExpr')
data('humanGeneInput')
x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneExpressionProfile=humanExpr)
class(x)