Description Usage Arguments Details Value Author(s) References Examples
Extract mutational signatures after the input Data and the input parameters have been checked andvalidated.
1 | extractSignatures(mutCountMatrix, params, bootStrap = TRUE)
|
mutCountMatrix |
numeric matrix of mutation counts |
params |
list including all parameters for performing the analysis |
bootStrap |
logical, shall bootstrapping be performed |
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.
list including the following elements
Wall: all extracted signatures
Hall: all extracted exposures
mutCounts.reconstructed: fitted values
mutCounts.errors: residuals
Damiano Fantini, damiano.fantini@gmail.com
More information and examples about mutational signature analysis can be found here:
GitHub Repo: https://github.com/dami82/mutSignatures/
More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/
Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/
Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6
WTSI framework: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588146/
1 2 3 4 | x <- mutSignatures:::getTestRunArgs("extractSignatures")
y <- mutSignatures:::extractSignatures(mutCountMatrix = as.matrix(x$muts),
params = as.list(x$params), bootStrap = TRUE)
y$Wk[1:10,]
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