ArrayExpressHTS: ExpressionSet for RNA-Seq experiment submitted in...
In ArrayExpressHTS: ArrayExpress High Throughput Sequencing Processing Pipeline

Description Usage Arguments Value Author(s) See Also Examples

View source: R/package.R

ArrayExpressHTS runs the RNA-Seq pipeline on a transcription profiling experiment available on the ArrayExpress database and produces an ExpressionSet R object. ArrayExpressHTS requires an Internet connection.

    ArrayExpressHTS( accession,
            options = list (
                    stranded           = FALSE,
                    insize             = NULL,
                    insizedev          = NULL,
                    reference          = "genome",
                    aligner            = "tophat",
                    aligner_options    = NULL,
                    count_feature      = "transcript",
                    count_options      = "",
                    count_method       = "cufflinks",
                    filter             = TRUE,
                    filtering_options  = NULL ),
            usercloud = TRUE,
            rcloudoptions = list (
                    nnodes     = "automatic",
                    pool       = c("4G", "8G", "16G", "32G", "64G"),
                    nretries   = 4 ),
            steplist = c("align", "count", "eset"),
            dir = getwd(),
            refdir = getDefaultReferenceDir(),
            want.reports = TRUE, 
            stop.on.warnings = FALSE )

`accession`	an ArrayExpress experiment accession identifier, e.g. "E-GEOD-16190"
`options`	defines pipeline options. See `getDefaultProcessingOptions`.
`usercloud`	defines if the R Cloud will be used to parallel experiment computation, if `FALSE`, experiment data files will be processed sequentially.
`rcloudoptions`	defines R Cloud options. See `getDefaultRCloudOptions`.
`steplist`	defines the steps the pipeline will perform.
`dir`	folder where experiment data will be stored and processed. Default is current directory.
`refdir`	the directory where reference data is located.
`want.reports`	defines if quality reports are produced. Reports usually make computation longer and eat up more memory. For faster computation use `FALSE`.
`stop.on.warnings`	self explanatory. Warnings are normally producesd when there are inconsistencies, which however would allow the result to be produced.

The output is an object of class ExpressionSet containing expression values in assayData (corresponding to the raw sequencing data files), the information contained in the .sdrf file in phenoData, the information in the adf file in featureData and the idf file content in experimentData.

If executed on a local PC, make sure that tools are available to the pipeline. Check prepareAnnotation to see what needs to be done to make tools available.

Andrew Tikhonov <andrew@ebi.ac.uk>, Angela Goncalves <angela.goncalves@ebi.ac.uk>

ArrayExpressHTSFastQ, prepareReference, prepareAnnotation, prepareAnnotation getDefaultProcessingOptions, getPipelineOptions,

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

    # if executed on a local PC, make sure tools
    # are available to the pipeline.
    expfolder = tempdir();
    
    # run the pipeline
    #
    aehts = ArrayExpressHTS("E-GEOD-16190", dir = expfolder);
    
    # load the expression set object
    loadednames = load(paste(expfolder, 
                        "/E-GEOD-16190/eset_notstd_rpkm.RData", sep=""));
    loadednames;

    get('library')(Biobase);

    # print out the expression values
    #
    head(assayData(eset)$exprs);

    # print out the experiment meta data 
    experimentData(eset);
    pData(eset);
}