extractSignatures {mutSignatures} | R Documentation |
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 |
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
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Wall: all extracted signatures
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Hall: all extracted exposures
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mutCounts.reconstructed: fitted values
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mutCounts.errors: residuals
Author(s)
Damiano Fantini, damiano.fantini@gmail.com
References
More information and examples about mutational signature analysis can be found here:
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GitHub Repo: https://github.com/dami82/mutSignatures/
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More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/
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Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/
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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/
Examples
x <- mutSignatures:::getTestRunArgs("extractSignatures")
y <- mutSignatures:::extractSignatures(mutCountMatrix = as.matrix(x$muts),
params = as.list(x$params), bootStrap = TRUE)
y$Wk[1:10,]