Download the metadata from all the projects. This can be useful for finding samples of interests across all projects.
all_metadata(subset = "sra", verbose = TRUE)Either sra, gtex or tcga. Specifies
which metadata file to download.
If TRUE it will print a message of where the file is
being downloaded to.
A DataFrame-class object with the phenotype metadata.
Note that for subset = 'gtex', there are more variables than
the ones we have for 'sra'. This information corresponds to file
GTEx_Data_V6_Annotations_SampleAttributesDS.txt available at
http://www.gtexportal.org/home/datasets. There you can find the
information describing these variables.
For TCGA we acquired metadata information from 3 different sources:
GDC: via a json query
CGC: via json queries and a custom script to merge the tables
TCGAbiolinks: we used to to parse GDC's XML files For more information, check https://github.com/leekgroup/recount-website/tree/master/metadata/tcga_prep.
metadata <- all_metadata()
#> 2023-05-07 05:53:14.435239 downloading the metadata to /tmp/RtmpDcoigj/metadata_clean_sra.Rdata