all_metadata: This function downloads the metadata for all projects.

In leekgroup/recount: Explore and download data from the recount project

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 4, 2024, 5:41 p.m.