fetch_geneset: Gene set fetch

Description Usage Arguments Value

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

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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 17, 2019, 8:35 a.m.