getTotalGeneNumber: Obtain the total number of genes in the given annotation...

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

A function to Obtain the total number of genes in the given annotation library.

Usage

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getTotalGeneNumber(categoryType=c('GO', 'GO.BP', 'GO.CC', 'GO.MF', 'DOLITE', 'KEGG', 'REACTOME.PATH'), known=TRUE, annotationLib=c('org.Ag.eg.db', 'org.Bt.eg.db', 'org.Ce.eg.db', 'org.Cf.eg.db', 'org.Dm.eg.db', 
							'org.Dr.eg.db', 'org.EcK12.eg.db', 'org.EcSakai.eg.db', 'org.Gg.eg.db', 'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Mmu.eg.db', 'org.Pt.eg.db', 'org.Rn.eg.db', 
							'org.Ss.eg.db', 'org.Xl.eg.db', 'org.At.tair.db', 'org.Pf.plasmo.db', 'org.Sc.sgd.db'))

Arguments

categoryType

name of given annotation category or NULL for user provided annotation list.

known

logic, specify only known annotation gene enrichment test.

annotationLib

name of given annotation library file or user provided annotation list.

Details

categoryType could be one of "GO", "GO.BP", "GO.CC", "GO.MF", "DOLITE", "KEGG" and "REACTOME.PATH".

annotationLib could be one of "org.Ag.eg.db", "org.Bt.eg.db", "org.Ce.eg.db", "org.Cf.eg.db", "org.Dm.eg.db", "org.Dr.eg.db", "org.EcK12.eg.db", "org.EcSakai.eg.db", "org.Gg.eg.db", "org.Hs.eg.db", "org.Mm.eg.db", "org.Mmu.eg.db", "org.Pt.eg.db", "org.Rn.eg.db", "org.Ss.eg.db", "org.Xl.eg.db", "org.At.tair.db", "org.Pf.plasmo.db" and "org.Sc.sgd.db". However, if caegoryType is set to "REACTOME.PATH", only 'org.At.tair.db'(516), 'org.Ce.eg.db'(627), 'org.Dm.eg.db'(686), 'org.EcK12.eg.db'(185), 'org.EcSakai.eg.db'(185), 'org.Gg.eg.db'(840), 'org.Hs.eg.db'(1019), 'org.Mm.eg.db'(900), 'org.Pf.plasmo.db'(308), 'org.Rn.eg.db'(883) and 'org.Sc.sgd.db'(473) are available. Since DOLITE is designed for human being, currently only 4051 genes are annotated in Disease Ontology. Other species could be mapped to homologous genes by getHomoGeneIDs.

If known is set to TRUE, the enrichment test only considers the genes with annotation. If FALSE, the total number of genes in that species will be returned.

Value

A number of total genes.

Author(s)

Gang Feng, Pan Du and Simon Lin

References

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

See Also

geneAnswersBuilder

Examples

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getTotalGeneNumber(categoryType='GO.CC', annotationLib='org.Hs.eg.db')

GeneAnswers documentation built on May 2, 2018, 2:55 a.m.