fetch_geo_datasets: fetch_geo_datasets

In AndrewC160/ROMOPOmics: ROMOPOmics: incorporating 'Omics Data Into The Observational Medical Outcomes Partnership (OMOP) Data Model

Description

Wrapper for most GEO import functions when incorporating GEOquery datasets. Given a GEO dataset ID (i.e. "GDS507") or list of such IDs, function retrieves S4 metadata obejcts from GEOquery for each dataset, its associated platform (GPL), series (GSE), and column data. Function also produces a metadata table for each such component, and stores these within nested list. A comprehensive metadata table is also produced and stored. If multiple IDs are submitted, these are imported recursively, and metadata from each is a merged into a comprehensive metadata table in the top-level list. Invalid ID entries are identified by checking the validity of their purported URL: if invalid, a warning message is displayed. With multiple IDs, these are added to a text object denoting which failed.

Usage

fetch_geo_datasets(geo_dataset_ids, data_dir = NULL)

Arguments

geo_dataset_ids	GEO dataset ID (e.g. "GDS507") or a list of such IDs.
data_dir	Directory into which retrieved data objects should be stored. NULL by default, in which case saved to memory in a temp folder.

AndrewC160/ROMOPOmics documentation built on Jan. 27, 2021, 6:57 p.m.