SynSigRun: 'SynSigRun': An easy-to-use package for non-experts which...

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

SynSigRun: An easy-to-use package for non-experts which runs software packages reproducibly with synthetic tumors generated by SynSigGen.

Description

SynSigRun gives necessary information to mutational-signature analysis programs. These programs used catalogs of synthetic mutational spectra created by package SynSigGen, and results were assessed by SynSigEval.

Workflow

Typical workflow for conducting a mutational signature analysis with mutational spectra is as follows.

Input mutational spectra

Mutational spectra can be obtained from vcf files of real samples (see "Importing mutational spectra from ICAMS"). Mutational spectra can also be generated in-silico by R package SynSigGen, and then imported by ICAMS (see "(In SynSigGen) Creating Synthetic Mutational Spectra").

Importing mutational spectra from ICAMS

Relevant functions are:

1. ReadCatalog

2. StrelkaSBSVCFFilesToCatalog

3. StrelkaIDVCFFilesToCatalog

4. MutectVCFFilesToCatalog

See ICAMS package documentation for more details.

(In SynSigGen) Creating Synthetic Mutational Spectra

These functions create synthetic mutational spectra based on parameters derived from mutational signature profiles and exposures.

Relevant functions for generate exposures are:

1. GenerateSynFromReal

2. GenerateSyntheticExposures

3. GenSBS1SBS5Exposure

After generating exposures for spectra dataset, SynSigGen used these functions to generate mutational spectra:

1. CreateFromReal

2. CreateMixedTumorTypeSyntheticData

3. CreateRandomSyn

See SynSigGen package documentation for more details.

(In SynSigRun) Run mutational analysis computational approaches

Relevant functions are:

1. RunhdpLessHier

2. Runmaftools

3. RunMutationalPatterns

4. RunsigneR

5. Runtcsm

(In SynSigEval) Summarize results

Summarize results of of signature extraction and exposure inference (a.k.a. signature attribution):

Relevant functions are:

1. SummarizeSigOnehelmsmanSubdir

2. SignatureAnalyzerSummarizeTopLevel

3. SignatureAnalyzerSummarizeSBS1SBS5

4. SummarizeSigOneSigProExtractorSubdir

5. SummarizeSigProExtractor

6. SummarizeSigOneExtrAttrSubdir

Package SynSigEval uses functions in ICAMSxtra to compare two sets of mutational signatures. Often we will be interested in comparing signature profiles extracted from synthetic data to the ground-truth signature profiles:

1. Match1Sig

2. MatchSigs1Direction

3. MatchSigs2Directions

4. MatchSigsAndRelabel

Folder structure for 9EEkWT1qgYnIfdHv6La1YuD0wXrJywz8-38- and 9EEkWT1qgYnIfdHv6La1YuD0wXrJywz8-39-:

Summary function will fit to the new 5-level folder structure:

First Level - top.level.dir: dataset folder (e.g. "S.0.1.Rsq.0.1", "syn.pancreas"). All spectra datasets under any top.level.dir have the same exposure.

Second Level - ground.truth.exposure.dir: spectra folder: (e.g. "sp.sp", "sa.sa.96"). All spectra datasets under any second.level.dir have the same signature and the same exposure counts.

Third Level - third.level.dir:

1. It can be ("Attr") for storing results of packages which can only do signature attribution of known signatures ("Attr");

2. It can be ("ExtrAttr"), folder to store results of computational approaches which can do de-novo extraction and following attribution, without knowing the number of ground-truth mutational signatures active in the spectra data set.

3. It can also be ("ExtrAttrExact"), folder to store results of computational approaches which can do de-novo extraction and following attribution, given the number of ground-truth mutational signatures active in the spectra data set.

Fourth Level - tool.dir: The results of a computational approach (e.g. "sigproextractor.results","SignatureEstimation.QP.results"). Under this level, tool.dir may contain multiple run.dir, each is a run of the computational approach using a specific number of seed.

Fifth level - run.dir: contains results from a run of the computational approach using a specific number of seed. (e.g. "seed.1")

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