obtain_enzyme: obtain_enzyme

View source: R/steps.R

obtain_enzymeR Documentation

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 May 31, 2024, 4:42 p.m.