findGene {cummeRbund} | R Documentation

## findGene

### Description

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.

### Usage

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

### Arguments

`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.

### Details

None.

### Value

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

### Note

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

### Author(s)

Loyal A. Goff

### References

None.

### Examples

    	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'

[Package cummeRbund version 2.28.0 Index]