findGene: findGene

In cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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'

cummeRbund documentation built on Nov. 8, 2020, 7:53 p.m.