Mapping homogenes for a GeneAnswers instance

Description

A function to mapping homogenes in all of slots of a GeneAnswer instance

Usage

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geneAnswersHomoMapping(x, species = c("human", "rat", "mouse", "fly"), speciesL = c("human", "rat", "mouse", "fly"), mappingMethod = c("direct", "biomaRt", "none"), filterGenes = NULL, verbose = TRUE)

Arguments

x

a GeneAnswers instance

species

species of the current genes

speciesL

species of the mapped genes

mappingMethod

mapping method, see details

filterGenes

a gene symbol vector to filter genes

verbose

logical, show current stage or not

Details

There are two mapping methods supported by current version. "direct" only works between human and mouse because most of human gene symbols are capitalized and only the first letter is uppercase for those homogenes in mouse. Another way is by means of package "biomaRt" ,which contains more information while the network connection is necessary to access biomaRt online server. Since two methods are based on different mechanisms, it is highly recommended to employ same method during mapping. Each method might introduce more homogenes, so users can remove ones that do not belong to original genes by optional "filterGeneList".

Value

return a mapped GeneAnswers instance

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

getHomoGeneIDs

Examples

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example(GeneAnswers)
## Not run: geneAnswersHomoMapping(x, species='human', speciesL='mouse', mappingMethod='direct')

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