DupChecker (version 1.10.2)

arrayExpressDownload: arrayExpressDownload

Description

The function downloads array express raw data from EBI ftp server based on datasets user provided. Once the compressed raw data is downloaded, individual target file will be extracted from compressed raw data. The dataset/count table will be returned.

Usage

arrayExpressDownload(datasets, targetDir = getwd(), filePattern = NULL, unzip = "internal", overwrite = FALSE)

Arguments

datasets

the dataset names, for example: c("E-TABM-43", "E-TABM-158")

targetDir

the target directory to store the datasets

filePattern

the file pattern of the expected data file extracted from gzipped file

unzip

the path to the command to be used in unzip function

overwrite

If TRUE, overwrite existing files, otherwise ignore such files.

Value

a data frame containing dataset and how many expected data files in that dataset

Examples

#download three datasets from ArrayExpress website
rootDir<-paste0(dirname(tempdir()), "/DupChecker")
dir.create(rootDir, showWarnings = FALSE)
datatable<-arrayExpressDownload(datasets = c("E-MEXP-3872"), targetDir=rootDir, filePattern="cel$")