download_study {recount} | R Documentation |
Download the gene or exon level RangedSummarizedExperiment-class objects provided by the recount project. Alternatively download the counts, metadata or file information for a given SRA study id. You can also download the sample bigWig files or the mean coverage bigWig file.
download_study(project, type = "rse-gene", outdir = project, download = TRUE, ...)
project |
A character vector with one SRA study id. |
type |
Specifies which files to download. The options are:
|
outdir |
The destination directory for the downloaded file(s).
Alternatively check the |
download |
Whether to download the files or just get the download urls. |
... |
Additional arguments passed to download. |
Check http://stackoverflow.com/a/34383991 if you need to find the effective URLs. For example, http://duffel.rail.bio/recount/DRP000366/bw/mean_DRP000366.bw points to a temporary link from Amazon Cloud Drive.
Returns invisibly the URL(s) for the files that were downloaded.
Leonardo Collado-Torres
## Find the URL to download the RangedSummarizedExperiment for the ## Geuvadis consortium study. url <- download_study('ERP001942', download = FALSE) ## See the actual URL url ## Download the example data included in the package for study SRP009615 url2 <- download_study('SRP009615') url2 ## Load the data load(file.path('SRP009615', 'rse_gene.Rdata')) ## Compare the data library('testthat') expect_equivalent(rse_gene, rse_gene_SRP009615)