arrayExpressDownload {DupChecker} | R Documentation |
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.
arrayExpressDownload(datasets, targetDir = getwd(), filePattern = NULL, unzip = "internal", overwrite = FALSE)
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. |
a data frame containing dataset and how many expected data files in that dataset
#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$")