enzyme: enzyme

View source: R/enzyme.R

enzymeR Documentation

enzyme

Description

Text mining the enzyme information.

Usage

enzyme(
  file,
  ecnum,
  onlyTerm = FALSE,
  onlyDf = FALSE,
  target = "abstract",
  taxec = FALSE,
  taxFile = NULL,
  candTax = NULL,
  argList = list(),
  apiKey = NULL
)

Arguments

file

file downloaded from expasy

ecnum

candidate ecnum, like those obtained from eggNOG-mapper

onlyTerm

only return quoted queries to wcAbst

onlyDf

only return ec description data.frame if onlyTerm and onlyDf are both specified, onlyTerm have priority

target

abstract or title

taxec

link taxonomy to EC using UniProt Taxonomy ID file If this is TRUE, data.frame is returned

taxFile

UniProt organism ID file path

candTax

when taxec=TRUE, search only for these species.

argList

passed to osplot(target="pubmed")

apiKey

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

object consisting of data frame and ggplot2 object

See Also

generalf

Examples

file <- "enzyme.dat"
## Not run: enzyme(file, ecnum="1.2.1.1")

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.