deconvolution_fit: deconvolution_fit

In FunGeST/Palimpsest: Package

deconvolution_fit

Description

Function to calculate the number and proportion of each SBS, DBS or indel signature in each sample, in addition to plotting each sample's mutational profile and its signature contribution.

Usage

deconvolution_fit(
  input_matrices = NULL,
  input_signatures = NULL,
  input_vcf = vcf,
  threshold = 6,
  signature_colours = sig_cols,
  doplot = TRUE,
  save_signatures_exp = TRUE,
  resdir = resdir
)

Arguments

input_matrices	Palimpsest input list of mutation number and proportion matrices.
input_signatures	Matrix of the mutational signatures to fit within the provided cohort of samples.
input_vcf	The VCF used in the current analysis. Only required when Type == "SBS" so that the strand bias of SBS mutations can be plotted.
threshold	Signatures contributing less then this percentage of total mutations within a sample will be discarded (e.g. if set to 6 and signature X contributes 5 per cent of a sample's mutations, signature X will not be reported as present in this sample).
signature_colours	Character vector of R-compatible colours representing each signature to be used graphical outputs. Each signature in input_signatures must have named colour in this vector for grpahical outputs to work. Use the "signature_colour_generator" function to generate colours for new signatures.
doplot	Logical indicating whether graphical outputs should be generated (defaults to TRUE).
save_signatures_exp	Logical indicating whether or not signatures_exp object should be saved in the redsir (defaults to TRUE).
resdir	Results directory.

Examples

signatures_exp <- deconvolution_fit(input_matrices = SBS_input, threshold = 8,input_signatures = SBS_liver,signature_colours = sig_cols,resdir = resdir)

FunGeST/Palimpsest documentation built on June 2, 2024, 4:21 a.m.