ABSOLUTE.summarize (v1)

Summarizes the results from multiple ABSOLUTE runs so that an analyst can manually review the solutions.

Author: Scott Carter, Matthew Meyerson, Gad Getz

Contact:

absolute-help@broadinstitute.org, http://www.broadinstitute.org/cancer/cga/cga_forums, gp-help@broadinstitute.org

Algorithm Version: ABSOLUTE 1.0.6

Summary

The ABSOLUTE.summarize module takes a file containing a list of ABSOLUTE output files (a collection of samples) and summarizes them in a format that facilitates the manual review of those results, including:

  • a tab-delimited table detailing the called results
  • plots of all the purity/ploidy modes
  • a plot for every uncalled result

Introduction

The purpose of ABSOLUTE is to extract the absolute copy number per cancer cell from a mixed DNA population of tumor and normal cells, where the tumor cells derive from a predominant clone line and some number of subclones.  ABSOLUTE uses segmented copy number data, together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations, to infer the purity (proportions of cells that are derived from the predominant tumor clone, from tumor subclones, and from normal cells) and the ploidy (the quantity of DNA in each cell) of the tumor.  The output of ABSOLUTE then provides the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.

Usage

The output of ABSOLUTE.summarize should be used by an analyst to judge whether to override the solutions supplied by ABSOLUTE.  See this page for more information on evaluating the solutions.

The finalized ABSOLUTE solutions can be selected with the ABSOLUTE.review module.

References

Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G.  Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012;30(5):413-21. (abstract and link to PDF)

Parameters

Name Description
collection name * A descriptive name for this collection of samples.  This is used for display and reporting purposes only.
absolute files * A group of ABSOLUTE RData output files from individual sample runs to be summarized together.
copy number type *

The copy number type to assess.  Options are:

  • allelic (default)
  • total
plot modes * Set this to FALSE to disable plotting of the purity/ploidy modes.  Default: TRUE

* - required

Input Files

  1. <absolute.files>
    A group of ABSOLUTE RData output files from individual sample runs to be summarized together.

Output Files

  1. <collection.name>_summary.PP-calls_tab.txt

A tab-delimited table detailing the called results.

  1. <collection.name>_summary.PP-modes.data.RData

A saved object named segobj.list that contains all information used to generate the other output files.  Also known as the modes file.

  1. <collection.name>_summary.PP-modes.plots.pdf

All plots of all of the purity/ploidy modes.  Only produced if the plot modes parameter is set to TRUE.

  1. *.ABSOLUTE_UNCALLED_PLOT.pdf

A plot for every uncalled result.

Example Data

A set of HAPSEG example data from the CGA group is available at:

ftp://ftp.broadinstitute.org/pub/genepattern/example_files/HAPSEG_1.1.1/paper_example.zip

This can be run through HAPSEG and the output supplied to ABSOLUTE.  Note that there is a README file in the ZIP archive that provides the filenames and parameters you will need to run this example data through HAPSEG, ABSOLUTE, ABSOLUTE.summarize, and ABSOLUTE.review.

Requirements

ABSOLUTE can only be used on the GenePattern public server, as it requires a specialized installation process that prevents distribution via the repository.  Please contact the authors listed above if you have an interest in installing ABSOLUTE locally.

The ABSOLUTE.summarize module runs only on GenePattern 3.4.2 or above and requires R2.15.2 with the following packages:

  • numDeriv_2012.9-1
  • getopt_1.17
  • optparse_0.9.5

Each of these R packages will be automatically downloaded and installed when the module is installed.  R2.15.2 must be installed and configured independently.

 

Platform Dependencies

Task Type:
SNP Analysis

CPU Type:
any

Operating System:
any

Language:
R2.15.2

Version Comments

Version Release Date Description
1 2013-06-30 Initial version.