bootstrapCancerGenomes: Bootstrap a Mutation Count Matrix.

In mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

Description

Rearrange a Mutation count Matrix using the multivariate normal distribution. The function returns a bootstrapped Mutation Count matrix whose dimensions are identical to the input matrix.

Usage

bootstrapCancerGenomes(genomes, seed = NULL)

Arguments

genomes	a numeric matrix of Mutation Counts. Rows correspond to Mutation Types, columns to different samples.
seed	integer, set a seed to obtain reproducible results. Defaulted to NULL

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

a numeric matrix of bootstrapped Mutation Counts. Rows correspond to Mutation Types, columns to different samples.

Author(s)

Damiano Fantini, [e-mail]

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

5. WTSI framework: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588146/

Examples

x <- cbind(c(10, 100, 20, 200, 30, 5), 
           c(100, 90, 80, 100, 11, 9))
mutSignatures:::bootstrapCancerGenomes(x)                

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