mutSignatures (version 2.1.1)

removeWeak: Remove Mutation Types Not Meeting the Threshold.

Description

Remove mutation types that account for a total number of mutations below a defined threshold.

Usage

removeWeak(input_mutCounts, params)

Arguments

input_mutCounts

numeric matrix of Mutation Counts

params

object (list) including all parameters required for running the analysis

Value

List including two elements:

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

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

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/

Examples

# NOT RUN {
x <- mutSignatures:::getTestRunArgs("removeWeak")
nrow(x$data)
y <- mutSignatures:::removeWeak(input_mutCounts = x$data, params = x$params)
nrow(y)
  
# }