gencode_annotation

Download and unzip annotation files from gencode
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/gencode_annotation.R (opens new window)
Data source: http://ftp.ebi.ac.uk/pub/databases/gencode/ (opens new window)

plot

Inputs

	label	type	description
species	species	string	'human' or 'mouse'
version	version	string	Character string. Case sensitive. must match available versions for each species under source URL link. e.g., 'M31' (species='mouse'), '42' (species='human')

Outputs

	label	type	description
annotation	annotation	File[]	the unzipped annotation file: gencode.v$version.annotation.gtf

Example:

## Get data from evaluting recipe
gencode_annotation <- recipeLoad('gencode_annotation')
gencode_annotation$species <- 'human'
gencode_annotation$version <- '42'
getData(gencode_annotation, outdir = 'data/folder', notes = c('gencode', 'annotation', 'human', '42'))

## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('gencode', 'annotation', 'human', '42'))

## Get data from Google bucket directly
dataUpdate('data/folder', cloud=TRUE)
dh <- dataSearch(c('gencode', 'annotation'))
getCloudData(dh[1], outdir = 'data/folder')