queryAE {ArrayExpress}R Documentation

XML query of the ArrayExpress repository

Description

queryAE queries ArrayExpress with keywords and give a list of ArrayExpress identifiers and their availability as raw and/or processed data, 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 character strings with all the ArrayExpress dataset identifiers which correspond to the query in the first column. The two following columns are filled with 'Yes' and 'No' according to the existence of raw and processed data.

Author(s)

Audrey Kauffmann Maintainer: <audrey@ebi.ac.uk>

See Also

ArrayExpress, getAE, magetab2bioc

Examples

## To retrieve all the identifiers of cancer data sets
Cancer = queryAE(keywords = "cancer")

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

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

[Package ArrayExpress version 1.2.3 Index]