annotateTargets.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/annotateTargets.R
\name{annotateTargets}
\alias{annotateTargets}
\title{Annotate targets with gene symbols}
\usage{
annotateTargets(x, txdb, org)
}
\arguments{
\item{x}{A \code{GRanges} object with interals to annotate}

\item{txdb}{A \code{TxDb} database, e.g.
\code{TxDb.Hsapiens.UCSC.hg19.knownGene}}

\item{org}{A \code{OrgDb} object, e.g. \code{org.Hs.eg.db}.}
}
\value{
A \code{GRanges} object.
}
\description{
This function can be used to add a \sQuote{Gene} meta column containing
gene symbols to a \code{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.
}
\examples{
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)

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

}
\author{
Markus Riester
}