fetch_geneset: Gene set fetch

In greenelab/ADAGEpath: ADAGE-based Signature Analysis

Gene set fetch

Description

Fetches gene sets from the Tribe webserver (urlhttps://tribe.greenelab.com). It can retrieve GO, KEGG, or user-created public gene sets for Pseudomonas aeruginosa.

Usage

fetch_geneset(type = "KEGG", username = NULL, access_date = NULL,
  max_size = Inf, min_size = 0)

Arguments

type	character, type of the gene sets, can be "GO", "KEGG", or "User" (default: "KEGG").
username	character, creator's TRIBE username (default: NULL)
access_date	character, in the format of month-day-year, the month and day should have two digits and the year should only contain the last two digits (e.g. 12-31-16). When specified, only the version of a term edited right before the access date is retrieved. In default, a term's most up-to-date version is retrieved. (default: NULL)
max_size	int, maximum gene set size to be considered as a meaningful gene set (default: Inf).
min_size	int, minimum gene set size to be considered as a meaningful gene set (default: 0).

Value

a named list with each element being a gene set

greenelab/ADAGEpath documentation built on May 25, 2022, 7:11 a.m.