load_raw: Load and annotate raw data downloaded from GEO.

In alexvpickering/crossmeta: Cross Platform Meta-Analysis of Microarray Data

Load and annotate raw data downloaded from GEO.

Description

Loads and annotates raw data previously downloaded with get_raw. Supported platforms include Affymetrix, Agilent, and Illumina.

Usage

load_raw(
  gse_names,
  data_dir = getwd(),
  gpl_dir = "..",
  overwrite = FALSE,
  ensql = NULL
)

Arguments

gse_names	Character vector of GSE names.
data_dir	String specifying directory with GSE folders.
gpl_dir	String specifying parent directory to search for previously downloaded GPL.soft files.
overwrite	Do you want to overwrite saved esets from previous load_raw?
ensql	For development. Path to sqlite file with ENTREZID and SYMBOL columns created in data-raw/entrezdt.

Value

List of annotated esets.

Examples

library(lydata)
data_dir <- system.file("extdata", package = "lydata")
eset <- load_raw("GSE9601", data_dir = data_dir)

alexvpickering/crossmeta documentation built on May 23, 2024, 5:06 a.m.