findPathways: Retrieve pathways by keywords

In datapplab/SBGNview: "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Retrieve pathways by keywords

Description

This function searches for pathways by input keywords.

Usage

findPathways(
  keywords = NULL,
  keywords.logic = "or",
  keyword.type = "pathway.name",
  org = NULL,
  SBGNview.data.folder = "./SBGNview.tmp.data"
)

Arguments

keywords	A character string or vector. The search is case in-sensitive.
keywords.logic	A character string. Options are 'and' or 'or' (default). This will tell the function if the search require 'all' or 'any' of the keywords to be present. It only makes difference when keyword.type is 'pathway.name'.
keyword.type	A character string. Either 'pathway.name' (default) or one of the ID types in data('mapped.ids')
org	A character string. The KEGG species code.
SBGNview.data.folder	A character string. Default: "./SBGNview.tmp.data". The path to a folder that will hold downloaded ID mapping files and pathway information data files.

Details

If 'keyword.type' is 'pathway.name' (default), this function will search for the presence of any keyword in the pathway.name column of data(pathways.info). The search is case in-sensitive. If 'keyword.type' is one of the identifier types and 'keywords' are corresponding identifiers, this function will return pathways that include nodes mapped to input identifiers.

Value

A dataframe. Contains information of pathways found.

Examples

data(pathways.info)
input.pathways <- findPathways('Adrenaline and noradrenaline biosynthesis')

datapplab/SBGNview documentation built on June 20, 2022, 9:55 p.m.