extractByGeneName: Extract subsets of refGenome by gene-name.

In refGenome: Gene and Splice Site Annotation Using Annotation Data from 'Ensembl' and 'UCSC' Genome Browsers

Description

The function takes objects derived from refGenome or refJunctions and returns a subset in which gene_name matches the given values. The returned object is of the same class as the given object.

Usage

extractByGeneName(object,geneNames,src,...)

Arguments

object

refGenome (or derived). Object from which subset is extracted.

geneNames

Character. Vector with gene names.

src	Unused within this package. Needed for compatibility reasons.

...

(unused)

Value

Same class as object

Author(s)

Wolfgang Kaisers

Examples

# + + + + + + + + + + + + + + + + + + #
# A) Extract from Genome
# + + + + + + + + + + + + + + + + + + #
ensfile<-system.file("extdata", 
                    "hs.ensembl.62.small.RData", package="refGenome")
ens<-loadGenome(ensfile)
ws7<-extractByGeneName(ens,"WASH7P")
ws7
# + + + + + + + + + + + + + + + + + + #
# B) Extract from splice junctions
# + + + + + + + + + + + + + + + + + + #
junc<-getSpliceTable(ens)
ddx<-extractByGeneName(junc,"DDX11L1")
ddx

refGenome documentation built on May 23, 2019, 1:03 a.m.