easyRNASeq annotation methods {easyRNASeq} | R Documentation

## Get genic annotation from a gff3/gtf file or using biomaRt

### Description

The annotation can be retrieved in two ways

- biomaRtUse biomaRt and Ensembl to get organism specific annotation.

- gff3/gtfUse a gff3 or gtf local annotation file.

- When using biomaRt, it is important that the `organism` argument to `AnnotParam` is set the prefix of one of the value available using the biomaRt `listDatasets` function, e.g. "Dmelanogaster".

- When reading from a gff3/gtf file, a version 3 formatted gff or a gtf (an Ensembl defined gff2 version) is expected. The function genomeIntervals `genomeIntervals-readGff3` is used to import the data.

### Usage

    ## S4 method for signature 'AnnotParam'
    getAnnotation(obj, verbose = FALSE, ...)

### Arguments

`obj` | An object of class `AnnotParam`
`verbose` | a boolean to turn on verbosity
`...` | See details

### Details

... are for additional arguments, passed to the biomaRt `getBM` function or to the `readGffGtf` internal function that takes an optional arguments: annotation.type that default to "exon". This is used to select the proper rows of the gff or gtf file.

### Value

A `GRanges` containing the fetched annotations.

### Author(s)

Nicolas Delhomme

### Examples

      ## Not run:
    	library("RnaSeqTutorial")
      getAnnotation(
        AnnotParam(
          organism="Dmelanogaster",
          datasource=system.file(
      		  "extdata",
    				"Dmel-mRNA-exon-r5.52.gff3",
    				package="RnaSeqTutorial"),
      		type="gff3"
      ))

    ## End(Not run)

[Package easyRNASeq version 2.24.1 Index]