mutSignatures (version 1.2)

setMutClusterParams: Set Parameters for Extracting Mutational Signatures

Description

Create an object (list) including all parameters required for running the mutSignatures framework

Usage

setMutClusterParams(num.processes.toextract = 2, tot.iterations = 4, 
tot.cores = 5, remove.weak.muttypes = 0.01, 
remove.last.percent = 0.07, process.distance = "cosine", 
tot.Replicates = 100, eps = 2.2204e-16, 
stopconv = 10000, niter = 1e+06)

Arguments

num.processes.toextract

number of signatures to extract

tot.iterations

number of iterations per core

tot.cores

number of cores to use for the analysis

remove.weak.muttypes

threshold for filtering out under-represented mutation types

remove.last.percent

threshold for removing outlier iteration results

process.distance

method for calculating distances. Default method is 'cosine'

tot.Replicates

number of replicates while checking stability

eps

close-to-zero numeric value for replacing zeros and preventing negative values in the matrix

stopconv

number of non-changing iterations before stopping NMF

niter

total number of terations for NMF

Value

Object (list) including all parameters for running the analysis

References

More info at: http://www.biotechworld.it/bioinf/2017/01/22/mutsignatures/

Examples

# NOT RUN {
setMutClusterParams()
# }