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Survival Analysis of mRNA Isoform Variation
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README.md

SURVIV: Survival Analysis of mRNA Isoform Variation

Requirements

  1. Install Python 2.6.x or Python 2.7.x and corresponding versions of NumPy and SciPy.
  2. Add the Python directory to the $PATH environment variable.

Installation:

The source code can be directly called from Python.

Usage:

$ python surviv.py input_read_count_file input_survival_file output_file

The examples of input files are available with the zipped source code. The input format is detailed in the Example section.

Example:

Test SURVIV on sample input: Run surviv.py as below to test the SURVIV script.

$ python surviv.py inc.txt surv.txt SURVIV_Result_P.txt

Input: Two input files are required for the SURVIV script. inc.txt: Each row of this input file contains an alternative splicing event. The 5 columns of this input file contain the read counts for the two isoforms of the alternative splicing event. The read counts for different patients are separated by commas in the column. As an example, for exon skipping events, each row defines a skipped exon and the columns contain the read counts for inclusion and skipping isoforms:

  • ID: User defined ID for the alternative splicing event.
  • IJC: inclusion junction counts, patients are separated by comma.
  • SJC: skipping junction counts, patients are separated by comma.
  • IncFormLen: length of inclusion form, used for normalization.
  • SkipFormLen: length of skipping form, used for normalization.

surv.txt: Each row of this input file contains the survival status for a patient. Important. The order of the patients in this file should match the order of patients in inc.txt. The 3 columns of this input file are:

  • PatientID: User defined ID for the patient.
  • Time: Follow up time.
  • Event: The status indicator, 0=alive, 1=dead.

Output: For each alternative splicing event, SURVIV outputs the P-values that evaluate the associations between alternative splicing and patient survival.

  • ID: User defined ID for the alternative splicing event.
  • IJC: inclusion junction counts, patients are separated by comma.
  • SJC: skipping junction counts, patients are separated by comma.
  • IncFormLen: length of inclusion form, used for normalization.
  • SkipFormLen: length of skipping form, used for normalization.
  • PValue: P-values of the alternative splicing event.

Contacts and bug reports

Yi Xing yxing@ucla.edu

Shihao Shen shihao@ucla.edu

If you found a bug or mistake in this project, we would like to know about it. Before you send us the bug report though, please check the following:

  1. Are you using the latest version? The bug you found may already have been fixed.
  2. Check that your input is in the correct format and you have selected the correct options.
  3. Please reduce your input to the smallest possible size that still produces the bug; we will need your input data to reproduce the problem, and the smaller you can make it, the easier it will be.

Publication

Shen S, Wang Y, Wang C, Wu YN, Xing Y. SURVIV: Survival Analysis of mRNA Isoform Variation. Nature Communications. (In press).

Copyright and License Information

Copyright (C) 2015 University of California, Los Angeles (UCLA) Shihao Shen and Yi Xing

Authors: Shihao Shen and Yi Xing

This program is licensed with commercial restriction use license. Please see the attached LICENSE file for details.

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