read_metadata: Read the metadata files

In LieberInstitute/recount3: Explore and download data from the recount3 project

Read the metadata files

Description

This function reads in the recount3 metadata files into R. You can first locate the files using locate_url() then download it to your computer using file_retrieve().

Usage

read_metadata(metadata_files)

Arguments

metadata_files

A character() with the local path to recount3 metadata files.

Value

A data.frame() with all lower case column names for the sample metadata.

See Also

Other internal functions for accessing the recount3 data: annotation_ext(), create_rse_manual(), file_retrieve(), locate_url_ann(), locate_url(), project_homes(), read_counts()

Examples

## Download the metadata files for project ERP110066
url_ERP110066_meta <- locate_url(
    "ERP110066",
    "data_sources/sra"
)
local_ERP110066_meta <- file_retrieve(
    url = url_ERP110066_meta
)

## Read the metadata
ERP110066_meta <- read_metadata(local_ERP110066_meta)
dim(ERP110066_meta)
colnames(ERP110066_meta)

## Read the metadata files for a project in a collection
## Note: using the test files since I can't access collections right now
## for this collection
ERP110066_collection_meta <- read_metadata(
    metadata_files = file_retrieve(
        locate_url(
            "ERP110066",
            "collections/geuvadis_smartseq",
            recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3"
        )
    )
)
dim(ERP110066_collection_meta)
## New columns for this collection
colnames(ERP110066_collection_meta)[!colnames(ERP110066_collection_meta) %in% colnames(ERP110066_meta)]

## Read the metadata for a mouse project
DRP002367_meta <- read_metadata(
    metadata_files = file_retrieve(
        locate_url("DRP002367", "data_sources/sra", organism = "mouse")
    )
)
dim(DRP002367_meta)

## Locate and read the GTEx bladder metadata
gtex_bladder_meta <- read_metadata(
    file_retrieve(
        locate_url("BLADDER", "data_sources/gtex")
    )
)

dim(gtex_bladder_meta)
colnames(gtex_bladder_meta)

LieberInstitute/recount3 documentation built on May 10, 2023, 6:01 a.m.