mgnify_get: Get MGnify info via the API

In leylabmpi/LeyLabRMisc: Ley Lab misc R functions, rmd templates, etc.

Get MGnify info via the API

Description

MGnify API: https://www.ebi.ac.uk/metagenomics/api/v1/

Usage

mgnify_get(
  accession = NULL,
  section = c("samples", "studies", "analyses", "biomes", "experiment-types"),
  search = NULL,
  lineage = NULL,
  instrument_platform = NULL,
  instrument_model = NULL,
  query = list(),
  max_pages = 1,
  base_url = "https://www.ebi.ac.uk/metagenomics/api/v1/",
  cache_file = "mgnify_request.RDS",
  cache_break = 10,
  use_cache = TRUE,
  ...
)

Arguments

accession	Study accession (primary or secondary). If provided, just info returned for that study.
section	Section of the API to query.
search	General keyword search to filter records.
lineage	Filter by lineage (eg., "root:Host-associated:Human").
query	List of additional queries provided to httr::GET.
max_pages	The maximum number of pages of records to return.
base_url	MGnify API base url
cache_file	File name to cache (checkpoint) the results. Useful for big queries in case the job is interuppted.
cache_break	Write cache file every N pages.
use_cache	Read the cache file, if it exists?
...	Parameters passed to httr::GET
instrutment_platform	Sequencing instrument platform (eg., "ILLUMINA").
instrutment_model	Sequencing instrument model (eg., "HiSeq" or "MiSeq").

Details

This function can query any "section" of the API (eg., "studies" or "samples").

Main filtering options are listed in the function (eg., lineage). More queries can be provides as a list via the query parameter. Note that not all filtering options for work each section. To see all filtering options for each section, click the "Filters" button at https://www.ebi.ac.uk/metagenomics/api/v1/samples

To prevent accidental big queries, only 1 page of results is returned by default (max_pages).

Value

data.frame

Examples

mgnify_get()
mgnify_get(search='soil')
mgnify_get(section='biomes')
mgnify_get(section='experiment-types')
mgnify_get(accession = 'ERP009004', section='studies')
mgnify_get(lineage='root:Host-associated', instrument_platform = 'ILLUMINA',
            instrument_model = 'HiSeq', max_pages=8)
mgnify_get(accession = 'SRS2472313')

leylabmpi/LeyLabRMisc documentation built on Nov. 3, 2022, 3:45 p.m.