prelimProcessAssess {mutSignatures}

Run a Preliminary Process Assess analysis.

Description

This function is an attempt to analyze the relationship between error and k. In other words, the goal of prelimProcessAssess is to visualize the reduction in the error/residuals

Usage

prelimProcessAssess(
  input,
  maxProcess = 6,
  approach = "counts",
  plot = TRUE,
  verbose = TRUE
)

Arguments

input

a mutationCounts-class object

maxProcess

integer, maximum k to test

approach

sting, "counts" or "freq"

plot

logical, shall a plot be printed to the active device

verbose

logical, info about the ongoing analysis be messaged/printed to console

Details

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

Value

a data.frame showing the estimated total error with respect to the range of k values

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