addWeak: Add Weak Mutation TYpes

In mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

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

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.

Value

Output is the final result of the deconvolution process

Author(s)

Damiano Fantini, [e-mail]

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/

mutSignatures documentation built on Nov. 9, 2020, 9:06 a.m.