deconvolution_fit: deconvolution_fit
In FunGeST/Palimpsest: Package

Description Usage Arguments Examples

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.

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
)

`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.

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