prepareAnnotation: Prepare annotation data for the RNA-Seq Pipeline

Description Usage Arguments Value Author(s) See Also Examples

View source: R/reference.R

Description

prepareAnnotation downloads the required annotation file for the selected organism from Ensembl and processes it so that it can be used by the pipeline. prepareAnnotation requires an Internet connection.

Usage

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    prepareAnnotation(organism, version = "current", 
        location = getDefaultReferenceDir(), refresh = FALSE, run = TRUE)

Arguments

organism

supported organism names can be viewed in the Ensemble database. Check 'ftp://ftp.ensembl.org/pub'.

version

"current" or other appropriate version. Check 'ftp://ftp.ensembl.org/pub'.

location

indicates where the annotation data should be stored.

refresh

if TRUE, existing annotation data will be rebuilt.

run

if FALSE, the commands to obtain and process the annotation will not be executed.

Value

The output is the version of the organism annotation that has been downloaded and processed. The annotation files are kept in the folder defined in location parameter.

Author(s)

Andrew Tikhonov <[email protected]>, Angela Goncalves <ange[email protected]>

See Also

ArrayExpressHTS, ArrayExpressHTSFastQ, prepareReference

Examples

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if (isRCloud()) { # disabled on local configs 
    # so as not to affect package building process
    
    par(ask = FALSE)

    # the following piece of code will take ~1.5 hours to complete
    #
    
    # if executed on a local PC, make sure tools are available
    # to the pipeline.
    # 
    
    # create directory
    #
    # Please note, tempdir() is used for automamtic test 
    # execution. Select directory more appropriate and 
    # suitable for keeping reference data.
    #
    referencefolder = paste(tempdir(), "/reference", sep = "")
    
    dir.create(referencefolder)
    
    # download and prepare annotation
    prepareAnnotation("Homo_sapiens", "current", location = referencefolder)
    prepareAnnotation("Mus_musculus", "NCBIM37.61", location = referencefolder)

}

ArrayExpressHTS documentation built on Nov. 17, 2017, 9:27 a.m.