easyRNASeq-annotation-methods: Get genic annotation from a gff3/gtf file or using biomaRt

In easyRNASeq: Count summarization and normalization for RNA-Seq data

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)

easyRNASeq documentation built on April 30, 2020, 2 a.m.