locate_url: Construct the URL to access a particular 'recount3' file
In LieberInstitute/recount3: Explore and download data from the recount3 project

locate_url

R Documentation

Construct the URL to access a particular `recount3` file

Description

Given an organism of interest, this function constructs the URL for accessing one of the output files from the recount3 project. You can then download the file using file_retrieve().

Usage

locate_url(
  project,
  project_home = project_homes(organism = organism, recount3_url = recount3_url),
  type = c("metadata", "gene", "exon", "jxn", "bw"),
  organism = c("human", "mouse"),
  sample = NULL,
  annotation = annotation_options(organism),
  jxn_format = c("ALL", "UNIQUE"),
  recount3_url = getOption("recount3_url", "http://duffel.rail.bio/recount3")
)

Arguments

`project`	A `character(1)` with the ID for a given study.
`project_home`	A `character(1)` with the home directory for the `project`. You can find these using `project_homes()`.
`type`	A `character(1)` specifying whether you want to access gene counts, exon counts, exon-exon junctions or base-pair BigWig coverage files (one per `sample`).
`organism`	A `character(1)` specifying which organism you want to download data from. Supported options are `"human"` or `"mouse"`.
`sample`	A `character()` vector with the sample ID(s) you want to download.
`annotation`	A `character(1)` specifying which annotation you want to download. Only used when `type` is either `gene` or `exon`.
`jxn_format`	A `character(1)` specifying whether the exon-exon junction files are derived from all the reads (`ALL`) or only the uniquely mapping read counts (`UNIQUE`). Note that `UNIQUE` is only available for some projects: GTEx and TCGA for human.
`recount3_url`	A `character(1)` specifying the home URL for `recount3` or a local directory where you have mirrored `recount3`. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be https://recount-opendata.s3.amazonaws.com/recount3/release from https://registry.opendata.aws/recount/ or SciServer datascope from IDIES at JHU https://sciserver.org/public-data/recount3/data. You can set the R option `recount3_url` (for example in your `.Rprofile`) if you have a favorite mirror.

Value

A character() with the URL(s) for the file(s) of interest.

Examples


## Example for metadata files from a project from SRA
locate_url(
    "SRP009615",
    "data_sources/sra"
)

## Example for metadata files from a project that is part of a collection
locate_url(
    "ERP110066",
    "collections/geuvadis_smartseq",
    recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3"
)

## Example for a BigWig file
locate_url(
    "SRP009615",
    "data_sources/sra",
    "bw",
    "human",
    "SRR387777"
)

## Locate example gene count files
locate_url(
    "SRP009615",
    "data_sources/sra",
    "gene"
)
locate_url(
    "SRP009615",
    "data_sources/sra",
    "gene",
    annotation = "refseq"
)

## Example for a gene count file from a project that is part of a collection
locate_url(
    "ERP110066",
    "collections/geuvadis_smartseq",
    "gene",
    recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3"
)

## Locate example junction files
locate_url(
    "SRP009615",
    "data_sources/sra",
    "jxn"
)

## Example for metadata files from a project from SRA
locate_url(
    "ERP001942",
    "data_sources/sra"
)

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