all_metadata: This function downloads the metadata for all projects.
In leekgroup/recount: Explore and download data from the recount project
all_metadata R Documentation
This function downloads the metadata for all projects.
Description
Download the metadata from all the projects. This can be useful for finding
samples of interests across all projects.
Usage
all_metadata(subset = "sra", verbose = TRUE)
Arguments
subset
Either sra, gtex or tcga. Specifies
which metadata file to download.
verbose
If TRUE it will print a message of where the file is
being downloaded to.
Details
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.
Value
A DataFrame-class object with the phenotype
metadata.
Author(s)
Leonardo Collado-Torres
Examples
metadata <- all_metadata()
leekgroup/recount documentation built on May 24, 2024, 11:19 a.m.
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| all_metadata | R Documentation |
This function downloads the metadata for all projects.
Description
Download the metadata from all the projects. This can be useful for finding samples of interests across all projects.
Usage
all_metadata(subset = "sra", verbose = TRUE)
Arguments
subset |
Either |
verbose |
If |
Details
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.
Value
A DataFrame-class object with the phenotype metadata.
Author(s)
Leonardo Collado-Torres
Examples
metadata <- all_metadata()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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