obtain_enzyme: obtain_enzyme

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

obtain_enzyme

Description

Obtain EC-related text data from PubMed

Usage

obtain_enzyme(
  file,
  ec_num,
  only_term = FALSE,
  only_df = FALSE,
  target = "abstract",
  tax_ec = FALSE,
  tax_file = NULL,
  cand_tax = NULL,
  arg_list = list(),
  api_key = NULL
)

Arguments

file	file downloaded from expasy
ec_num	candidate ecnum, like those obtained from eggNOG-mapper
only_term	only return quoted queries to pubmed
only_df	only return ec description data.frame if onlyTerm and onlyDf are both specified, onlyTerm have priority
target	abstract or title
tax_ec	link taxonomy to EC using UniProt Taxonomy ID file If this is TRUE, data.frame is returned
tax_file	UniProt organism ID file path
cand_tax	when taxec=TRUE, search only for these species.
arg_list	passed to obtain_pubmed()
api_key	api key for PubMed

Details

Query the Enzyme Comission number and obtain description, and search pubmed for these enzymes and make word cloud and correlation network. Need to specify the path to "enzyme.dat" downloaded from from ExPASy (https://enzyme.expasy.org/).

Value

biotext class object

See Also

generalf

noriakis/wcGeneSummary documentation built on April 22, 2024, 7:12 a.m.