buildAnnotationStore {recoup} | R Documentation

## 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.

### Author(s)

Panagiotis Moulos

### Examples

        buildAnnotationStore("mm9","ensembl")

[Package recoup version 1.15.1 Index]