annotateTargets {PureCN} | R Documentation

## Annotate targets with gene symbols

### Description

This function can be used to add a ‘Gene’ meta column containing gene symbols to a `GRanges` object. It applies heuristics to find the protein coding genes that were likely meant to target in the assay design in case transcripts overlap.

### Usage

    annotateTargets(x, txdb, org)

### Arguments

`x` | A `GRanges` object with interals to annotate
`txdb` | A `TxDb` database, e.g. `TxDb.Hsapiens.UCSC.hg19.knownGene`
`org` | A `OrgDb` object, e.g. `org.Hs.eg.db`.

### Value

A `GRanges` object.

### Author(s)

Markus Riester

### Examples

    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    library(org.Hs.eg.db)

    normal.coverage.file <- system.file("extdata", "example_normal.txt",
        package="PureCN")
    x <- head(readCoverageFile(normal.coverage.file),100)
    x <- annotateTargets(x,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db)

[Package PureCN version 1.12.2 Index]