get.mol.list: Retrieve gene list or compound list from collected databases

In chemokine/OmicsSBGN: Overlay omics data onto SBGN pathway diagram

Description

Retrieve gene list or compound list from collected databases

Usage

get.mol.list(database = "pathwayCommons",
  mol.list.ID.type = "ENTREZID", org = "hsa", cpd.or.gene = "gene",
  output.pathway.name = TRUE, combine.duplicated.set = TRUE,
  truncate.name.length = 50,
  SBGNview.data.folder = "./SBGNview.tmp.data")

Arguments

database	Character string. The database where gene list will be extracted. Acceptable values: "MetaCyc", "pathwayCommons", "MetaCyc". The value is case in-sensitive.
mol.list.ID.type	Character string. The ID type of output gene list. One of the supported types in data("mapped.ids")
org	Character string. The three letter species code used by KEGG. E.g. "hsa","mmu"
cpd.or.gene	Character string. One of "gene" or "compound"
output.pathway.name	Logical. 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. 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. The pathway names will be truncated to at most that length.
SBGNview.data.folder	A character string. The path to a folder that will hold download ID mapping files and pathway information data files. The data can be reused once downloaded.

Value

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

chemokine/OmicsSBGN documentation built on June 27, 2019, 7:52 p.m.