enzyme: enzyme

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

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 April 22, 2024, 7:12 a.m.