compileMetadata: compileMetadata

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

compileMetadata

Description

Compiles metadata for a single dataset that includes sample and sample metadata. Note that this function uses memoised functions to speed up loops. If something changes in gemma as you work and you want to update, restart your session or use forgetGemmaMemoised

Usage

compileMetadata(
  dataset,
  collapseBioMaterials = TRUE,
  outputType = c("data.frame", "list"),
  memoised = TRUE
)

Arguments

dataset	Character. Can either be the dataset ID or its short name (e.g. GSE1234).
collapseBioMaterials	If TRUE collapses samples into biomaterials Some datasets represent
outputType	data.frame or list. A data.frame will return a single data frame including experiment and sample data. List output will return a list of length 2 where experiment and sample data are separated.
memoised	Should memoisation be used for base API calls. Useful if calling a large number of datasets in succession, defaults to TRUE. Use forgetGemmaMemoised to clear memory.

Value

A data.frame.

Examples

compileMetadata('GSE11322')
compileMetadata(1017)

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