package-options: Functions to work with package level options
In ArrayExpressHTS: ArrayExpress High Throughput Sequencing Processing Pipeline

Description Usage Arguments Details Value Author(s) See Also Examples

Functions to work with ArrayExpressHTS package level options.

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    getPipelineOptions()
    getPipelineOption(name, default = NULL, options = defaultOptions)
    setPipelineOptions(...)

`...`	a list ot options to set.
`name`	name of the option to return. In order to see all options, use `getPipelineOptions`;
`default`	default values in case the option is not defined
`options`	options environment, by default the ArrayExpresHTS environment;

These are the basic functions to get and set pakcage options and perform necessary reinitialization following the change in required.

getPipelineOptions returns an environment where ArrayExpressHTS options are stored.

setPipelineOptions sets one or a number of ArrayExpressHTS options.

Please note that the following options are used to store locations of external tools used by the package: "ArrayExpressHTS.bowtie", "ArrayExpressHTS.tophat", "ArrayExpressHTS.bwa", "ArrayExpressHTS.cufflinks", "ArrayExpressHTS.mmseq", "ArrayExpressHTS.samtools", etc.

If any of the options needs to be changed, use setPipelineOption(...) to make necessary chnages. Following the change, PATH environment varibale automatically gets updated as necessary.

Please note that the package supports only certain versions of tools. Other versions may not be fully compatible, and if used, this can result in errors on certain steps of the pipeline. The list of supported versions can be obtained using getPieplineOption(...) with the corresponding tool option, e.g. "ArrayExpressHTS.bowtie". Not supported versions can be used at user's own risk.

getPipelineOption returns ArrayExpressHTS option specified by option name. If option is not defined the specified default value will be returned.

The output is the environment where pipeline options are stored.

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

getDefaultProcessingOptions, ArrayExpressHTS, ArrayExpressHTSFastQ

    # get options
    pipelineOptions = getPipelineOptions()
    
    # list all names
    ls(pipelineOptions)
    
    # set pipeline options
    setPipelineOptions("trace" = "disabled", "memorymonitor" = "disabled");
    
    # get options
    getPipelineOption("trace");
    getPipelineOption("memorymonitor");