mutSignatures (version 2.1.1)

filterOutIterations: Remove Iterations that Generated Outlier Results.

Description

Internal function from the WTSI framework, ported to R. This is a core function called from within a deconvoluteMutCounts() call. This function removes iterations that generated outlier results.

Usage

filterOutIterations(wall, hall, cnt_errors, cnt_reconstructed, params)

Arguments

wall

numeric matrix combining w results from all iterations

hall

numeric matrix combining h results from all iterations

cnt_errors

numeric matrix combining all residuals from all iterations

cnt_reconstructed

numeric matrix combining fitted values from all iterations

params

list including alll parameters for running the analysis

Value

list including all data required for running the subsequent stability check

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/