getAnnotation: Get Gemma annotations

In PavlidisLab/gemmaAPI.R: A wrapper for Gemma's restful API

Get Gemma annotations

Description

Gets Gemma's platform annotation files that can be accessed from https://gemma.msl.ubc.ca/annots/

Usage

getAnnotation(
  platform,
  annotType = c("bioProcess", "noParents", "allParents"),
  file = NULL,
  return = TRUE,
  overwrite = FALSE
)

Arguments

platform	Can either be the platform ID or its short name (e.g: GPL1355). Retrieval by ID is more efficient. Only platforms that user has access to will be available.
annotType	Which go terms should the input include
file	Character. File path. If provided, response will be saved to file
return	Logical. If the response should be returned. Set to false when you only want to save a file
overwrite	Logical. If TRUE, existing files will be overwritten. If FALSE a warning will be thrown and no action is taken.

Value

A data frame including annotation information

PavlidisLab/gemmaAPI.R documentation built on July 26, 2022, 7:13 a.m.