recoup (version 1.0.2)

buildAnnotationStore: Build a local annotation database for recoup

Description

This function creates a local annotation database to be used with recoup so as to avoid long time on the fly annotation downloads and formatting.

Usage

buildAnnotationStore(organisms, sources,
    home = file.path(path.expand("~"), ".recoup"),
    forceDownload = TRUE, rc = NULL)

Arguments

organisms

a character vector of organisms for which to download and build annotations. Check the main recoup help page for details on supported organisms.

sources

a character vector of public sources from which to download and build annotations. Check the main recoup help page for details on supported annotation sources.

home

a valid path (accessible at least by the current user) where the annotation database will be set up. It defaults to ".recoup" inside the current user's home directory.

forceDownload

by default, buildAnnotationStore will not download an existing annotation again (FALSE). Set to TRUE if you wish to update the annotation database.

rc

fraction (0-1) of cores to use in a multicore system. It defaults to NULL (no parallelization). It is used in the case of type="exon" to process the return value of the query to the UCSC Genome Browser database.

Value

• The function does not return anything. Only the annotation directory and contents are created.

Examples

buildAnnotationStore("mm9","ensembl")