findGene: findGene
In shiauck/cummeRbund_on_RSQLite2.0: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Description Usage Arguments Details Value Note Author(s) References Examples

A helper function to retrieve the gene_ids given a 'lookup' value (e.g. gene_short_name, isoform_id, etc). Utility to search for gene_id and gene_short_name given a single 'query' string (e.g. query='pink1' will return all genes with 'pink1' (case-insensitive) in the gene_short_name field.

1 2	## S4 method for signature 'CuffSet' findGene(object, query)

`object`	An object of class 'CuffSet' (Primary 'pointer' object for Cufflinks data).
`query`	A character string for which you would like to retrieve corresponding gene_id values.

None.

Returns a data.frame of gene_id and gene_short_name values corresponding to genes from which 'query' matches

Right now, this does not return an error if it cannot find a gene. (this is probably a bad thing...)

Loyal A. Goff

None.

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	cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create master CuffSet object
	myQuery<-'pink1'
	findGene(cuff,myQuery) # Retrieve gene_id values for any genes matching 'pink1'