prepareAnnotation: Prepare annotation data for the RNA-Seq Pipeline

In andrewtikhonov/ArrayExpressHTS: ArrayExpress High Throughput Sequencing Processing Pipeline

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

    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 <[e-mail]>, Angela Goncalves <[e-mail]>

See Also

ArrayExpressHTS, ArrayExpressHTSFastQ, prepareReference

Examples

    
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)

}

andrewtikhonov/ArrayExpressHTS documentation built on May 28, 2019, 4:57 p.m.