Description Usage Arguments Details Value Author(s) Examples
View source: R/download_study.R
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.
1 2 3 4 5 6 7 8 | download_study(
project,
type = "rse-gene",
outdir = project,
download = TRUE,
version = 2,
...
)
|
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. |
version |
A single integer specifying which version of the files to
download. Valid options are 1 and 2, as described in
https://jhubiostatistics.shinyapps.io/recount/ under the
documentation tab. Briefly, version 1 are counts based on reduced exons while
version 2 are based on disjoint exons. This argument mostly just matters for
the exon counts. Defaults to version 2 (disjoint exons).
Use |
... |
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 link from SciServer.
Transcript quantifications are described in Fu et al, bioRxiv, 2018. https://www.biorxiv.org/content/10.1101/247346v2
FANTOM-CAT/recount2 quantifications are described in Imada, Sanchez, et al., bioRxiv, 2019. https://www.biorxiv.org/content/10.1101/659490v1
Returns invisibly the URL(s) for the files that were downloaded.
Leonardo Collado-Torres
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## Find the URL to download the RangedSummarizedExperiment for the
## Geuvadis consortium study.
url <- download_study("ERP001942", download = FALSE)
## See the actual URL
url
## Not run:
## 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)
## End(Not run)
|
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