frequencize {mutSignatures} | R Documentation |
Convert Mutation COunts to PerMille Frequencies.
Description
Convert Mutation COunts to frequencies. Typically, a permille frequence is returned. In other words, the resulting number indicates the expected mutation count if the genome hat a total of 1000 mutations. This way, the MutSignatures analysis will be less biased toward the hyper-mutator samples.
Usage
frequencize(countMatrix, permille = TRUE)
Arguments
countMatrix |
numeric matrix of mutation counts |
permille |
ligucal, shall the permille conversion be used instead of the standard frequency |
Details
This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.
Value
list including colSums (mutation burden of each sample) and freqs (matrix of frequencies)
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
Examples
A <- cbind(c(7, 100, 90, 1000), c(1, 3, 5, 9))
fA <- mutSignatures::frequencize(A)
fA$freqs