annotateTargets: Annotate targets with gene symbols

In PureCN: Copy number calling and SNV classification using targeted short read sequencing

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)

PureCN documentation built on Nov. 8, 2020, 5:37 p.m.