Go Back

TCGA.Merge - version 1

24 October 2011 - Robert Borkowski, robert.borkowski@utsouthwestern.edu

twitter: @rborkows

A module for collating TCGA Level 3 expression data, distributed in a one-file-per-sample format to a single, tab-delimited file with one probe per row, and one column per sample.

Be sure to check for proper line endings! Use the RXCtoGCT module to transform the output into a full-fledged .gct file.

Parameters: 

“input”: An archive (tested with .zip) containing BOTH the “file_manifest.txt” generated by TCGA during the data download, and each of the sample files you wish to collate.

“output”: The desired output file name. Will have “.txt” appended.

Known issues:

-Leaves behind the uncompressed .txt files.

Language:
any
Operating System:
any
Original Author:
Robert Borkowski, University of Texas Southwestern Medical Center
Uploaded by:
rborkows on October 24, 2011 12:04
Version Comment:
v1\: Now works by extracting an archive with the file manifest and per sample files.