arrayExpressDownload: arrayExpressDownload

In DupChecker: a package for checking high-throughput genomic data redundancy in meta-analysis

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$")

DupChecker documentation built on April 28, 2020, 6:46 p.m.