Man pages for steverozen/SynSigGen
Create Catalogs of Synthetic Mutational Spectra
| AddAllScripts | Create scripts to run SignatureAnalyzer in all subdirectories... |
| AddNoise | Exposures and spectra with Poisson or negative binomial noise... |
| AddScript | Add an R script to run SignatureAnalyzer a particular... |
| AssignPresentAbsentOneSample | Randomly assign present / absent to each of a set of... |
| BladderSkin1000 | Generate synthetic data sets modeled on bladder TCC and skin... |
| Create1CatRandomExpRandomSigs | Create a catalog of "random" synthetic spectra for 96-channel... |
| Create.2.7a.7b.Abstract | This function supersedes the second part of... |
| Create.3.5.40.Abstract | Create synthetic spectra based on SBS3 SBS5 SBS40 |
| CreateAndWriteCatalog | Create and write a mutational spectra catalog |
| CreateFromReal | Create a specific synthetic data set based on real exposures... |
| CreateMeanAndStdevForSigs | Create means and standard deviations of log10 mutation counts... |
| CreateMixedTumorTypeSyntheticData | Create a test data set based on >= 1 tumor types. |
| CreateNumSigsPerTumor | Create 'num.exposures' signature counts from a normal... |
| CreateOnePairOfRandomCatalogs | Create a pair of "random" synthetic catalogs, one for... |
| CreateOneRandomMutSigProfile | Create one "random" artificial signature profile. |
| CreateRandomExposures | Create synthetic exposure data. |
| CreateRandomMutSigProfiles | Create a matrix of "random" signature profiles. |
| CreateRandomSAAndSPSynCatalogs | Create a full SignatureAnalyzer / SigProfiler test data set... |
| CreateRandomSyn | This is the top-level function to create a set of spectra... |
| CreateSBS1SBS5CorrelatedSyntheticData | Function to generate 20 SBS1-SBS5-correlated Synthetic... |
| CreateSBS1SBS5CorrelatedSyntheticDataOneDataset | Wrapper function for generating SBS1-SBS5-correlated... |
| CreateSynCatalogs | Generate synthetic spectra catalogs given signature profiles... |
| Diff4SynDataSets | diff new directory / files against regression data for... |
| ExposureNums2Exposures | Select 'num.exp' signatures from the members of 'sig.names'... |
| GenerateAllRandomSA | Generate a full set of random data with characteristics... |
| GenerateAllRandomSP | Generate a suite of data with random signatures and... |
| GenerateListOfSigParams | Generate a list of signature parameters for different cancer... |
| GenerateNoisyTumors | Generate noisy tumors from available exposures |
| GenerateSynAbstract | Generate synthetic exposures from abstract parameters. |
| GenerateSynExposureOneSample | Using parameters given to generate exposures for synthetic... |
| GenerateSynFromReal | Generate synthetic exposures from real exposures. |
| GenerateSyntheticExposures | Create synthetic exposures based given parameters |
| GenerateSyntheticTumors | Generate synthetic tumors based on real exposures in one or... |
| GenerateSyntheticTumorsFromSigParams | Generate synthetic tumors based on signature parameters in... |
| GenSBS1SBS5Exposure | Generate correlated exposures for multiple tumors Wrapper... |
| GenSBS1SBS5ExposureOneTumor | Generate correlated exposures for one tumor Function to... |
| GetSynSigParamsFromExposures | Empirical estimates of key parameters describing exposures... |
| ManyTypes2700 | Create a specific synthetic data set of 2,700 tumors. |
| MapSPToSASignatureNamesInExposure | With the signatures represented in a matrix of exposures,... |
| Merge2Exposures | Merge 2 exposure matrices |
| MergeExposures | Merge all exposure matrices in a list of matrices |
| MutationalSignatures | Reference mutational signature profiles from PCAWG7. |
| NewCreateAndWriteCatalog | Create and write a mutational spectra catalog |
| NewDiff4SynDataSets | Diff two directories or files. |
| OLD.SplitCatCOMPOSITE | Split COMPOSITE (SNS1536+DBS78+ID83) catalogs in 'ICAMS'... |
| OutDir | Create file names in a given directory |
| PancAdenoCA1000 | Create 1000 synthetic pancreatic adenocarcinoma spectra. |
| ParametersSALike | Parameters for generating data with exposures resembling... |
| ParametersSPLike | Parameters for generating data with exposures resembling... |
| PlotCorrelationScatterplot | Plot scatter plot for correlation between two vectors.... |
| PlotCorrelationScatterplotForExposures | Plot scatter plot for correlation between exposures of two... |
| present.sigs | Decide which signatures will be present in the catalogs of... |
| RCCOvary1000 | Create synthetic spectra based on renal cell carcinoma and... |
| ReadCatCOMPOSITE | Read a COMPOSITE catalog |
| ReadExposure | Read an exposure matrix from a file |
| ReadSynapseExposure | Read an exposure matrix from a Synapse file |
| RealExposures | Real exposure (signature attributions) from SignatureAnalyzer... |
| SAAndSPSynDataOneCAType | Generate parallel synthetic exposures from real SA and SP... |
| SBS1SBS5datasetNames | Names of datasets generated by... |
| SBS1SBS5parameter | Parameters used to generate synthetic spectra with correlated... |
| signature.params | Empirical signature parameters of PCAWG7 platinum tumor... |
| SynSigGen | SynSigGen |
| SynSigParamsOneSignature | Extract parameters for one mutational signature profile |
| WriteCatCOMPOSITE | Write a COMPOSITE catalog or signature matrix to disk |
| WriteExposure | Write exposure matrix to a file |
| WriteSynSigParams | Write key parameters describing exposures due to a signature... |
| xFixSASigNames | Standardize SignatureAnalyzer signature names. |
