NEWS.md

In WuyangFF95/SynSigRun: Run Mutational Signature Analysis Software Packages Using Mutational Spectra generated by SynSigGen

SynSigRun 1.0.0

• Cleaned in folder "data-raw/"
• Cleaned duplicate files already in package SynSigGen

• Sorted and re-numbered running scripts into folders named with authors of manuscripts.

• Clarified README.md. The two purposes of the package are:

• Wrap signature analysis package runs in R functions to simplify execution for non-expert users.

• Contain all necessary scripts to reproduce results from earlier benchmarking results in Rozen Lab.

• Simplified dependencies in DESCRIPTION

SynSigRun 0.1.2

Added

• Added 4.join.combined.extraction.results.Wlicoxon.R in folder data-raw/scripts.for.SBS1SBS5. This script is for combining csv files which summarizes extraction measures. In order to obtain such csv files, users should run scripts in data-raw/scripts.for.SBS1SBS5/3a_evaluation_without_knowing_K and data-raw/scripts.for.SBS1SBS5/3b_evaluation_given_K.
• Fixed bugs in RunmutSignatures() Runmaftools() RunMutationalPatterns

SynSigRun 0.1.1

Fixed

In RunSomaticSignatures(): Fixed the unused parameter CPU.cores Fixed the bug which spawns too many processes and exceeds ulimit in Linux. * Fixed error in calculation of second derivative of RSS.

SynSigRun 0.0.5

Added

Added scripts at data-raw/scripts.for.SBS1SBS5 for running computational approaches with synthetic tumor datasets generated by SynSigGen::CreateSBS1SBS5CorrelatedSyntheticData (requires SynSigGen version 1.0.4).

• 1_data_generation - Generates 20 SBS1-SBS5 datasets at data-raw/ or other repositories.
• 2_running_approaches - running computational approaches using SynSigRun wrapper functions, and output results as a 5-level folder structure:
• 2a_running_approaches_without_knowing_K - runnning with number of ground-truth signatures (K) unspecfied
• 2b_running_approaches_given_K - running with K specified as 2
• 3_evaluation - evaluating performance of signature extraction by calling evaluation functions in SynSigEval.
• 3a_evaluation_without_knowing_K
• 3b_evaluation_given_K

SynSigRun 0.0.1.90xx

Added

• Created README.md and reference manual.
• Added biocViews and Remotes as field name in the DESCRIPTION.

WuyangFF95/SynSigRun documentation built on Oct. 7, 2022, 1:16 p.m.