sbgn.gsets: Retrieve gene list or compound list from collected databases

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

Description

Retrieve gene list or compound list from collected databases

Usage

sbgn.gsets(
  id.type = "ENTREZID",
  mol.type = "gene",
  species = "hsa",
  database = "pathwayCommons",
  output.pathway.name = TRUE,
  combine.duplicated.set = TRUE,
  truncate.name.length = 50,
  SBGNview.data.folder = "./SBGNview.tmp.data"
)

Arguments

id.type	A character string. Default: "ENTREZID". The ID type of output gene list. One of the supported types in data('mapped.ids')
mol.type	A character string. Default: "gene". One of 'gene' or 'cpd'
species	A character string. Default: "hsa". The three letter species code used by KEGG. E.g. 'hsa','mmu'
database	A character string. Default: "pathwayCommons". The database where gene list will be extracted. Acceptable values: 'MetaCyc', 'pathwayCommons', 'MetaCrop'. The value is case in-sensitive.
output.pathway.name	Logical. Default: T. If set to 'TRUE', the names of returned list are in the format: 'pathway.id::pathway.name'. If set to 'FALSE', the format is 'pahtway.id'
combine.duplicated.set	Logical. Default: T. Some pathways have the same geneset. If this parameter is set to 'TRUE', the output list will combine pathways that have the same gene set. The name in the list will be pathway names concatinated with '||'
truncate.name.length	Integer. Default: 50. The pathway names will be truncated to at most that length.
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.

Value

A list. Each element is a genelist of a pathway.

Examples

data(pathways.info)
mol.list <- sbgn.gsets(id.type = 'ENTREZID',
                       species = 'hsa',
                       database = 'pathwayCommons')
  

SBGNview documentation built on March 3, 2021, 2 a.m.