addGeneAnnotation,CopyNumberBreakPoints-method {GeneBreak} | R Documentation |
Maps features to gene locations.
## S4 method for signature 'CopyNumberBreakPoints' addGeneAnnotation(object, geneAnnotation)
object |
An object of class CopyNumberBreakPoints |
geneAnnotation |
An object of class |
The end of the first feature after gene start location up to and including the first feature after gene end location will be defined as gene-associated feaures. For hg18, hg19 and hg38 built-in gene annotation files obtained from ensembl can be used. Please take care to use a matching reference genome for your breakpoint data. In stead of using the built-in gene annotion files, feature-to-gene mapping can be based on an user-defined annotion file. The dataframe should contain at least these four columns: "Gene", "Chromosome", "Start" and "End".
Returns an object of class CopyNumberBreakPointGenes with gene annotation added.
data( copynumber.data.chr20 ) data( ens.gene.ann.hg18 ) ## other buil-in gene annotations are: # data( ens.gene.ann.hg19 ) # data( ens.gene.ann.hg38 ) bp <- getBreakpoints( copynumber.data.chr20 ) bp <- bpFilter( bp ) # input copynumber.data.chr20 is hg18 based bp <- addGeneAnnotation( bp, ens.gene.ann.hg18 ) ## options to inspect the data bp accessOptions( bp )