These functions will be deprecated. Please use other functions instead.

Usage

mgnify_client(
  username = NULL,
  password = NULL,
  usecache = FALSE,
  cache_dir = NULL,
  warnings = FALSE,
  use_memcache = FALSE,
  ...
)

mgnify_query(
  client,
  qtype = "samples",
  accession = NULL,
  asDataFrame = TRUE,
  maxhits = 200,
  usecache = FALSE,
  ...
)

mgnify_analyses_from_samples(client, accession, usecache = TRUE, ...)

mgnify_analyses_from_studies(client, accession, usecache = TRUE, ...)

mgnify_get_download_urls(
  client,
  accessions,
  accession_type,
  usecache = TRUE,
  ...
)

mgnify_download(
  client,
  url,
  file = NULL,
  read_func = NULL,
  usecache = TRUE,
  Debug = FALSE,
  ...
)

mgnify_get_analyses_results(
  client = NULL,
  accessions,
  retrievelist = c(),
  compact_results = TRUE,
  usecache = TRUE,
  bulk_dl = FALSE,
  ...
)

mgnify_get_analyses_phyloseq(
  client = NULL,
  accessions,
  usecache = TRUE,
  returnLists = FALSE,
  tax_SU = "SSU",
  get_tree = FALSE,
  ...
)

mgnify_get_analyses_metadata(client, accessions, usecache = TRUE, ...)

mgnify_retrieve_json(
  client,
  path = "biomes",
  complete_url = NULL,
  qopts = NULL,
  maxhits = 200,
  usecache = FALSE,
  Debug = FALSE,
  ...
)

Arguments

username: -
password: -
usecache: -
cache_dir: -
warnings: -
use_memcache: -
...: -
client: -
qtype: -
accession: -
asDataFrame: -
maxhits: -
accessions: -
accession_type: -
url: -
file: -
read_func: -
Debug: -
retrievelist: -
compact_results: -
bulk_dl: -
returnLists: -
tax_SU: -
get_tree: -
path: -
complete_url: -
qopts: -

These functions will be deprecated. Please use other functions instead.

Usage

Arguments

Value