mutSignatures (version 2.1.1)

addWeak: Add Weak Mutation TYpes

Description

Restore Mutation Types that were initially excluded because a low number of total counts.

Usage

addWeak(
  mutationTypesToAddSet,
  processes_I,
  processesStd_I,
  Wall_I,
  genomeErrors_I,
  genomesReconstructed_I
)

Arguments

mutationTypesToAddSet

Set of mutations to restore

processes_I

Set of Mutational Processes

processesStd_I

Set of standard deviations of all Mutational Processes

Wall_I

Set of all W matrices previously extracted

genomeErrors_I

Set of all residuals

genomesReconstructed_I

Fitted Values according to the most likely Model

Value

Output is the final result of the deconvolution process

Details

This is one of the core functions included in the original mutSignatures R library, and in the WTSI MATLAB framework. This is an internal function.

References

More information and examples about mutational signature analysis can be found here:

1. GitHub Repo: https://github.com/dami82/mutSignatures/

2. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

3. Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/

4. Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6

5. WTSI framework: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588146/