findGene

Share:

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

1
2
## 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

1
2
3
	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'

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.