Reconstruct a catalogue from a signature

Generates reconstructed substitution profile (catalogues) generated by proportionally combining each estimated contribution.

Usage

sig_reconstruct(signature, n)

Arguments

signature

a data.frame in sigverse signature format

n

total number of variants to use for reconstruction

Value

data.frame conforming to sigverse catalogue format

Examples

library(sigstash)

# Load a signature collection
signatures <- sig_load("COSMIC_v3.3.1_SBS_GRCh38")

# Create a model that represents a mix of SBS1 (40%) and SBS2 (60%)
model <- c(SBS1 = 0.4, SBS2 = 0.6)

# Add selected signatures to the combined model
combined_signatures <- sig_combine(signatures, model)

# Flatten the combined_signatures dataframe that keeps separate signatures
signature <- sig_combine_collapse_to_single_signature(combined_signatures)

# Reconstruct a perfect catalogue describing what the mutational profile of a sample
# with 200 mutations and the given signature model would look like
reconstuction <- sig_reconstruct(signature, n=200)

# Visualise Result
# sig_visualise(reconstuction, class = "catalogue")