annotateTranscripts {bumphunter} | R Documentation

## Annotate transcripts

### Description

Annotate transcripts

### Usage

    annotateTranscripts(txdb, annotationPackage = NULL, by = c("tx","gene"), codingOnly=FALSE, verbose = TRUE, requireAnnotation = FALSE, mappingInfo = NULL, simplifyGeneID = FALSE)

### Arguments

`txdb` | A `TxDb` database object such as `TxDb.Hsapiens.UCSC.hg19.knownGene`
`annotationPackage` | An annotation data package from which to obtain gene/transcript annotation. For example `org.Hs.eg.db`. If none is provided the function tries to infer it from `organism(txdb)` and if it can't it proceeds without annotation unless `requireAnnotation = TRUE`.
`by` | Should we create a `GRanges` of transcripts (`tx`) or genes (`gene`).
`codingOnly` | Should we exclude all the non-coding transcripts.
`verbose` | logical value. If 'TRUE', it writes out some messages indicating progress. If 'FALSE' nothing should be printed.
`requireAnnotation` | logical value. If 'TRUE' function will stop if no annotation package is successfully loaded.
`mappingInfo` | a named list with elements 'column', 'keytype' and 'multiVals'. If specified this information will be used with mapIds when mapping the gene ids using `annotationPackage`. This is useful when working with a `txdb` object from ENSEMBL or GENCODE among other databases.
`simplifyGeneID` | logical value. If 'TRUE', gene ids will be shortened to before a dot is present in the id. This is useful for changing GENCODE gene ids to ENSEMBL ids.

### Details

This function prepares a `GRanges` for the `matchGenes` function. It adds information and in particular adds exons information to each gene/transcript.

### Value

A `GRanges` object with an attribute `description` set to `annotatedTranscripts`. The following columns are added. `seqinfo` is the information returned by `seqinfo`, `CSS` is the coding region start, `CSE` is the coding region end, `Tx` is the transcript ID used in TxDb, `Entrez` is the Entrez ID, `Gene` is the gene symbol, `Refseq` is the RefSeq annotation, `Nexons` is the number of exons, `Exons` is an `IRanges` with the exon information.

### Author(s)

Harris Jaffee and Rafael A. Irizarry. 'mappingInfo' and 'simplifyGeneID' contributed by Leonardo Collado-Torres.

### See Also

`matchGenes`

### Examples

    ## Not run:
        library("TxDb.Hsapiens.UCSC.hg19.knownGene")
        genes <- annotateTranscripts(TxDb.Hsapiens.UCSC.hg19.knownGene)

        ##and to avoid guessing the annotation package:
        genes <- annotateTranscripts(TxDb.Hsapiens.UCSC.hg19.knownGene,annotation="org.Hs.eg.db")

    ## End(Not run)

[Package bumphunter version 1.22.0 Index]