queryAE: XML query of the ArrayExpress repository

In ArrayExpress: Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Description

queryAE queries the ArrayExpress database with keywords and give a dataframe with ArrayExpress identifiers and related information, as an output.

Usage

queryAE(keywords = NULL, species = NULL)

Arguments

keywords	the keyword(s) of interest. To use several words, they must be separated by a "+" as shown in the examples.
species	the specie(s) of interest.

Value

A dataframe with all the ArrayExpress dataset identifiers which correspond to the query in the first column. The following columns contain information about these datasets, such as the number of raw files, the number of data processed, the release date on the database, the pubmed ID, the species, the experiment design and the experimental factors.

Author(s)

Ibrahim Emam, Audrey Kauffmann

Maintainer: <[e-mail]>

See Also

ArrayExpress, getAE

Examples

## To retrieve all the identifiers of pneumonia data sets
pneumo = queryAE(keywords = "pneumonia")

## To retrieve all the identifiers of pneumonia data sets studied in human
pneumoHS = queryAE(keywords = "pneumonia", species = "homo+sapiens")

ArrayExpress documentation built on Nov. 8, 2020, 6:26 p.m.