prepare_geo: Download and Process GEO Data

In easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

Download and Process GEO Data

Description

This function downloads gene expression data from the Gene Expression Omnibus (GEO) database. It retrieves either the expression matrix or the supplementary tabular data if the expression data is not available. The function also allows for the conversion of probe identifiers to gene symbols and can combine multiple probes into a single symbol.

Usage

prepare_geo(geo, dir = ".", combine = TRUE, method = "max")

Arguments

geo	A character string specifying the GEO Series ID (e.g., "GSE12345").
dir	A character string specifying the directory where files should be downloaded. Default is the current working directory (".").
combine	A logical value indicating whether to combine multiple probes into a single gene symbol. Default is TRUE.
method	A character string specifying the method to use for combining probes into a single gene symbol. Options are "max" (take the maximum value) or "mean" (compute the average). Default is "max".

Value

A list containing:

data	A data frame of the expression matrix.
sample	A data frame of the sample metadata.
feature	A data frame of the feature metadata, which includes gene symbols if combining probes.

easybio documentation built on Sept. 17, 2024, 1:08 a.m.