frequencize: Convert Mutation COunts to PerMille Frequencies.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/s03_all_functions.R

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

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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:

  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

Examples

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A <- cbind(c(7, 100, 90, 1000), c(1, 3, 5, 9))
fA <- mutSignatures::frequencize(A)
fA$freqs
 

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