easyRNASeq (version 2.8.2)

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

Description

The annotation can be retrieved in two ways

• biomaRt

{Use biomaRt and Ensembl to get organism specific annotation.} gff3/gtf{Use a gff3 or gtf local annotation file.}

Usage

## S3 method for class 'AnnotParam':
getAnnotation(obj, verbose = FALSE, ...)

Arguments

obj

An object of class AnnotParam

verbose

a boolean to turn on verbosity

...

See details

Value

• A GRanges containing the fetched annotations.

itemize

• When usingbiomaRt, it is important that theorganismargument toAnnotParamis set the prefix of one of the value available using thebiomaRtlistDatasetsfunction, e.g. "Dmelanogaster".

item

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 readGff3 is used to import the data.

pkg

biomaRt

code

readGffGtf

Details

...

Examples

library("RnaSeqTutorial")
  getAnnotation(
    AnnotParam(
      organism="Dmelanogaster",
      datasource=system.file(
  		  "extdata",
				"Dmel-mRNA-exon-r5.52.gff3",
				package="RnaSeqTutorial"),
  		type="gff3"
  ))