deprecate: These functions will be deprecated. Please use other...
In beadyallen/MGnifyR: R interface to EBI MGnify metagenomics resource

deprecate

R Documentation

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

Description

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`	-