BatchDownload: BatchDownload
In GEOsearch: GEOsearch
Description
Usage
Arguments
Details
Value
Author(s)
Examples
View source: R/BatchDownload.R
Description
Generate shell file to download the SRA of multiple GSE or GSM
Usage
1
BatchDownload(namelist, GSMdownloadpath = ".")
Arguments
namelist
A character list of GSE or GSM ID.
GSMdownloadpath
A character value specifying the path to download the SRA files on users own Linux/Unix computer.
Details
This function returns a shell file that can download the SRA of multiple GSE or GSM. The shell file should be run on user's own computer with Linux/Unix system and wget installed.
The download process is to set up a bunch of directories under the path specified by users (GSMdownloadpath) and download the SRA files inside the paths.
Note: it is the users' job to make sure the GSE and GSM names are correct. Otherwise the function will run forever due to inner error control system.
Also, it could take a long time for the function to complete if there are lots of GSE series in namelist.
Value
A character string of commands to be run on users' computer.
Author(s)
Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>
Examples
1
BatchDownload("GSM1274542")
GEOsearch documentation built on Nov. 17, 2017, 8:37 a.m.
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Description Usage Arguments Details Value Author(s) Examples
View source: R/BatchDownload.R
Description
Generate shell file to download the SRA of multiple GSE or GSM
Usage
1 | BatchDownload(namelist, GSMdownloadpath = ".")
|
Arguments
namelist |
A character list of GSE or GSM ID. |
GSMdownloadpath |
A character value specifying the path to download the SRA files on users own Linux/Unix computer. |
Details
This function returns a shell file that can download the SRA of multiple GSE or GSM. The shell file should be run on user's own computer with Linux/Unix system and wget installed. The download process is to set up a bunch of directories under the path specified by users (GSMdownloadpath) and download the SRA files inside the paths. Note: it is the users' job to make sure the GSE and GSM names are correct. Otherwise the function will run forever due to inner error control system. Also, it could take a long time for the function to complete if there are lots of GSE series in namelist.
Value
A character string of commands to be run on users' computer.
Author(s)
Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>
Examples
1 | BatchDownload("GSM1274542")
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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