extractByGeneID: Extract subsets of refGenome by gene-ID.

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

extractByGeneId(object,geneids,...)

Arguments

object

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

geneids

Character. Vector with gene ID's.

...

(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)
ddx<-extractByGeneId(ens,"ENSG00000223972")
ddx
# + + + + + + + + + + + + + + + + + + #
# B) Extract from splice junctions
# + + + + + + + + + + + + + + + + + + #
junc<-getSpliceTable(ens)
ddx<-extractByGeneId(junc,"ENSG00000223972")
ddx

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