setMutClusterParams {mutSignatures}

Set Parameters for Extracting Mutational Signatures.

Description

Create an object including all parameters required for running the mutSignatures framework.

Usage

setMutClusterParams(
  num_processesToExtract = 2,
  num_totIterations = 10,
  num_parallelCores = 1,
  thresh_removeWeakMutTypes = 0.01,
  thresh_removeLastPercent = 0.07,
  distanceFunction = "cosine",
  num_totReplicates = 100,
  eps = 2.2204e-16,
  stopconv = 20000,
  niter = 1e+06,
  guided = TRUE,
  debug = FALSE,
  approach = "freq",
  stopRule = "DF",
  algorithm = "brunet",
  logIterations = "lite",
  seed = 12345
)

Arguments

num_processesToExtract

integer, number of mutational signatures to extract

num_totIterations

integer, total number of iterations (bootstrapping)

num_parallelCores

integer, number of cores to use for the analysis

thresh_removeWeakMutTypes

numeric, threshold for filtering out under-represented mutation types

thresh_removeLastPercent

numeric, threshold for removing outlier iteration results

distanceFunction

string, method for calculating distances. Default method is "cosine"

num_totReplicates

integer, number of replicates while checking stability

eps

numeric, close-to-zero positive numeric value for replacing zeros and preventing negative values to appear in the matrix during NMF

stopconv

integer, max number of stable iterations before termination. Defaults to 20000.

niter

integer, max number of iterations to run. Defaults to 1000000

guided

logical, shall clustering be guided to improve aggregation upon bootstrapping

debug

logical, shall the analysis be run in DEBUG mode

approach

string, indicating whether to model absolute counts ("counts") or per_mille frequency ("freq"). Defaults to "freq".

stopRule

= string, use the sub-optimal termination rule ("AL") from the WTSI package (actually, iterations won't terminate, so niter will most certainly reached) or our efficient termination rule ("DF"). Defaults to "DF". The "AL" option is implemented for compatibility reasons, but not recommended.

algorithm

string, algorithm to be used for NMF. Set to "brunet", or "alexa" for using the standard algorithm (Brunet's), otherwise the alternative "chihjen" algorithm will be used.

logIterations

string indicating if storing and returining all intermediates, or only final results. Defaults to "lite", i.e. returns full output and limited intermediates. Alternatively, set to "full".

seed

integer, seed to set for reproducibility

Value

Object including all parameters for running the analysis

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

library(mutSignatures) 
# defaults params
A <- setMutClusterParams()
A
# A second example, set num_processes
B <- setMutClusterParams(num_processesToExtract = 5)
B