Finalizes solutions of absolute copy number and multiplicity for a collection of tumor samples. Used after ABSOLUTE and ABSOLUTE.summarize.
Author: Scott Carter, Matthew Meyerson, Gad Getz
Algorithm Version: ABSOLUTE 1.0.6
The ABSOLUTE.review module finalizes selected solutions originally modeled by ABSOLUTE. It takes the original or a modified version of the calls output file (*.PP-calls_tab.txt) and the modes file (*.PP-modes.data.RData) from ABSOLUTE.summarize and provides finalized results for each sample in the collection.
You manually review solutions from ABSOLUTE results and annotate the calls table file from ABSOLUTE.summarize with the desired solutions. To continue with top ranked solutions for all the samples, provide the unmodified file directly to ABSOLUTE.review.
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)
|reviewed pp calls file *||The annotated calls file either directly or modified from an ABSOLUTE.summarize module run.|
|analyst id *||A display name of the analyst who selected alternate solutions for the calls file for record keeping.|
|modes file *||The <collection.name>.PP-modes.data.RData file produced by ABSOLUTE.summarize. Contains data for all the plotted solutions of the ABSOLUTE analysis.|
|collection name *||A descriptive name for this collection of samples. Can vary from the collection name used in the ABSOLUTE.summarize module run.|
|copy number type *||
The copy number type to assess. This should match the parameter used in ABSOLUTE.
* - required
The collection name corresponds to that supplied to ABSOLUTE.review. The <sample.name> field corresponds to that supplied in the original ABSOLUTE module run.
The module runs only on GenePattern 3.4.2 or above and requires R2.15 with the following packages, each of which will automatically download and install when the module is installed:
Please install R2.15.3 instead of R2.15.2 before installing the module. The GenePattern team has confirmed test data reproducibility for this module using R2.15.3 compared to R2.15.2 and can only provide limited support for other versions. The GenePattern team recommends R2.15.3, which fixes significant bugs in R2.15.2, and which must be installed and configured independently as discussed in Using Different Versions of R and Using the R Installer Plug-in. These sections also provide information on patch level fixes that are necessary when additional installations of R are made and considerations for those who use R outside of GenePattern.
|1.4||2015-10-13||Updated to make use of the R package installer.|