mutSignatures (version 2.1.1)

frequencize: 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

Value

list including colSums (mutation burden of each sample) and freqs (matrix of frequencies)

Details

This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.

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

# NOT RUN {
A <- cbind(c(7, 100, 90, 1000), c(1, 3, 5, 9))
fA <- mutSignatures::frequencize(A)
fA$freqs
 
# }