all_metadata {recount} | 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()

[Package recount version 1.20.0 Index]