mutSignatures (version 2.1.1)

extractSignatures: Extract Signatures from Genomic Mutational Catalogs.

Description

Extract mutational signatures after the input Data and the input parameters have been checked andvalidated.

Usage

extractSignatures(mutCountMatrix, params, bootStrap = TRUE)

Arguments

mutCountMatrix

numeric matrix of mutation counts

params

list including all parameters for performing the analysis

bootStrap

logical, shall bootstrapping be performed

Value

list including the following elements

1. Wall: all extracted signatures

2. Hall: all extracted exposures

3. mutCounts.reconstructed: fitted values

4. mutCounts.errors: residuals

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("extractSignatures")
y <- mutSignatures:::extractSignatures(mutCountMatrix = as.matrix(x$muts), 
                                       params = as.list(x$params), bootStrap = TRUE)
y$Wk[1:10,]


# }