downloadAE: Downloading microarray data from ArrayExpress database

In EwaMarek/FindReference: Find reference genes or miRNAs basing on microarray data.

Description

downloadAE function downloads microarray data from ArrayExpress database basing on experiment identifiers. Then it identifies microarray platform on which the experiment was performed using downloaded .sdrf file.

Usage

downloadAE(ExpInfoTable, path)

Arguments

path	A character indicating directory where data should be downloaded and extracted.
ExpIds	A data frame with two columns named Experiment and RawData. The first column should contain experiment identifiers from ArrayExpress database to download. In the RawData column there should be a character "T" or "F" for each experiment, where "T" means that downloaded data should be raw type and "F" for processed type.

Details

The output of this function is needed later in load_multi_data and load_data functions and that's why it is also saved in dataAE.rds which could be easy loaded with readRDS.

Value

Function returns a list of lists where the first one contains names of downloaded files (the output from getAE function from ArrayExpress package) and saves it as dataAE.rds. In the second list .sdrf files are stored in which there are information about samples and experiment conditions. The third element of returned list is a data.frame with information about platform for each experiment.

Examples

## Not run: downloadAE(c("E-GEOD-65292", "E-TABM-90"), getwd())

## Not run: experiments_ids = c("E-GEOD-65292", "E-TABM-90")
downloadAE(experiments_ids, getwd())
## End(Not run)

EwaMarek/FindReference documentation built on May 30, 2019, 3:40 p.m.