frequencize: Convert Mutation COunts to PerMille Frequencies.

In dami82/mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

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, [e-mail]

References

More information and examples about mutational signature analysis can be found here:

1. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

2. 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

dami82/mutSignatures documentation built on Jan. 24, 2023, 12:21 a.m.