mgnify_get | R Documentation |
MGnify API: https://www.ebi.ac.uk/metagenomics/api/v1/
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,
...
)
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"). |
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).
data.frame
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')
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