NEWS.md

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

SynSigGen 1.1.1

Fixed

• Fixed a bug in function GenerateNoisyTumors to only write signatures that are present in exposures to CSV file.

Added

• Added new dependency packages cosmicsig and mSigAct.

SynSigGen 1.1.0

Backward compatibility fix

Due to fix in function GenerateSynExposureOneSample to round the mutations due to each signature in version 1.0.9, the wrapper functions to generate data sets for Nature paper and SBS1-SBS5 paper fail to reproduce the data sets used by these papers.

In SynSigGen 1.1.0, we disabled the rounding of mutations due to each signature when running generator functions for legacy data sets, so that these legacy data sets can be reproduced.

Updated

• Updated documentation for argument sig.params in function GenerateSyntheticExposures.

Added

• Added two fields URL and BugReports in DESCRIPTION.

SynSigGen 1.0.13

Removed

• Removed exported data ID.MMR.params because the list of MSI-H tumors is not complete when generating the old data.

SynSigGen 1.0.12

Update

• Updated exported function MergeExposures to sort the signature ids of the merged exposure.

• Suppressed warning messages that came from internal function NumFromId.

Bug fix

• Fixed bug in internal function GetMutationType to check all the signature names to determine the mutation type.

SynSigGen 1.0.11

Important Update

• Updated exported function GetSynSigParamsFromExposures and internal function SynSigParamsOneSignature to only use the size parameter from empirical signature parameters if there is only one data to fit the negative binomial distribution. The mu parameter will be using the original mutation count.

SynSigGen 1.0.10

Updated

• Updated function GenerateSyntheticTumors to show informative messages about regenerating parameters from the synthetic exposures and compare with that from real exposures if verbose > 0.

Added

• Added new argument tumor.marker.name in function GenerateSyntheticTumors.

• Added new argument sig.params in exported functions GetSynSigParamsFromExposures and GenerateSyntheticTumors.

• Added two new exported functions GenerateListOfSigParams and GenerateSyntheticTumorsFromSigParams.

SynSigGen 1.0.9

Updated

• Updated function GenerateSynExposureOneSample to round the synthetic exposure to make it biologically reasonable.

• Updated function GetSynSigParamsFromExposures not to drop rare signatures that are present in only one sample when distribution is neg.binom. Instead, this function will use the empirical signature parameters from all cancer types.

• Updated function GenerateSyntheticTumors to enable generating different number of synthetic tumors for each cancer type.

• Updated function GetSynSigParamsFromExposures to drop signatures which do not have empirical signature parameters from all cancer types.

• Updated function GenerateSyntheticTumors and GenerateNoisyTumors to append mutation type information to the names of files generated.

• Updated function GenerateSyntheticExposures to remove signatures that have zero exposure in the synthetic data.

Added

• Added default value 100 for argument n.binom.size in function AddNoise.

• Added new exported data signature.params.

• Added new exported data ID.MMR.params.

• Added two new internal functions NumFromId and SortSigId.

Fixed

• Fixed a bug in function GenerateSynExposureOneSample to round the mutations due to each signature.

SynSigGen 1.0.8

Added

• Added new exported function GenerateNoisyTumors.

• Minor change to function GenerateSyntheticTumors for always writing the signature names in the parameters CSV file in case some signature is not present in the synthetic data.

SynSigGen 1.0.7

Added

• Added new argument distribution in functions SynSigParamsOneSignature and GetSynSigParamsFromExposures to enable fitting the exposures using negative binomial distribution.

• Added new argument distribution and sig.params in function GenerateSynExposureOneSample to enable generating synthetic exposures using negative binomial distribution.

• Added new argument distribution in function GenerateSyntheticExposures to enable generating synthetic exposures using negative binomial distribution.

• Added new exported function GenerateSyntheticTumors which enables generating synthetic tumors using negative binomial distribution.

• Added new argument verbose in function GenerateSyntheticTumors which can cat various messages if value greater than 0.

• Added new argument cancer.type in function GetSynSigParamsFromExposures.

Fixed

• Fixed a bug in function SynSigParamsOneSignature to generate parameter estimates (negative binomial distribution) for one signature only using those tumors which have mutations for this particular signature.

Updated

• Updated function SynSigParamsOneSignature to return NA for the parameter estimates (negative binomial distribution) for one signature if there is only one tumor which has mutation for this particular signature.

SynSigGen 1.0.6

Added

• Added data object "SBS1SBS5datasetNames" as names of SBS1-SBS5 spectra datasets generated by CreateSBS1SBS5CorrelatedSyntheticData()

• Added new argument sig.matrix in functions GenerateSynExposureOneSample and GenerateSyntheticExposures so that we can resample the synthetic exposures to make sure the total mutations for the reconstructed catalog is not zero.

Fixed

• Fixed a bug in GetSynSigParamsFromExposures when the exposures only have one row that are not all zeros.

SynSigGen 1.0.5

Simplified

• Simplified folder structure of SBS1-SBS5-correlated dataset, generated by CreateSBS1SBS5CorrelatedSyntheticData() - The files of synthetic datasets are under the dataset folders, and no more sp.sp folders.

SynSigGen 1.0.4

Last version generates SBS1-SBS5-correlated dataset with two-layer directory structure:

• Name of dataset (e.g. S.0.1.Rsq.0.1)
• Folder sp.sp, means that two ground-truth signatures (SBS1 and SBS5) are from results of SigProfiler in (https://doi.org/10.1038/s41586-020-1943-3)
• Files of synthetic datasets.

Clarified

• Clarified package README
• Clarified package documentation
• Clarified function documentation

Fixed typo

• Renamed function Create.3.4.40.Abstract() to Create.3.5.40.Abstract()

SynSigGen 1.0.3

• Removed R/SigSimilarity.R (functionality now in ICAMSxtra) and adjusted code in this package.

SynSigGen 1.0.2.9001

Added

• Added function AddNoise.
• Added biocViews as a field name in package DESCRIPTION.
• Created reference manual.

steverozen/SynSigGen documentation built on April 1, 2022, 8:54 p.m.