extractSignatures: Extract Signatures from Genomic Mutational Catalogs.

In mutSignatures: Decipher Mutational Signatures from Somatic 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

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

list including the following elements

1. Wall: all extracted signatures

2. Hall: all extracted exposures

3. mutCounts.reconstructed: fitted values

4. mutCounts.errors: residuals

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/

Examples

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

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