Maps features to gene locations.
## S4 method for signature 'CopyNumberBreakPoints' addGeneAnnotation(object, geneAnnotation)
An object of class CopyNumberBreakPoints
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.
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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 )
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