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Last data update: 2014.03.03

R: Build a local annotation database for recoup

buildAnnotationStore

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")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(recoup)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: ggplot2
Loading required package: ComplexHeatmap
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/recoup/buildAnnotationStore.Rd_%03d_medium.png", width=480, height=480)
> ### Name: buildAnnotationStore
> ### Title: Build a local annotation database for recoup
> ### Aliases: buildAnnotationStore
> 
> ### ** Examples
> 
> ## No test: 
>     buildAnnotationStore("mm9","ensembl")
Retrieving genome information for mm9
Retrieving gene annotation for mm9 from ensembl
Retrieving exon annotation for mm9 from ensembl
Merging exons for mm9 from ensembl