Identify the most likely combination of known mutational signatures which explain the mutational profile observed in a sample of interest.
Arguments
- catalogue
catalogue of mutations observed in your sample. A named vector where names are channel and values are counts.
- signatures
a channel X signature matrix where values represent fractional contributions of each channels.
- method
how should fitting be performed. nnls: Use non-negative least squares method
Value
a named vector with 1 element per signature. Values indicate the estimated number of mutation drawn from that signature.
Examples
observed_counts <- c(
"C>A" = 183,
"C>G" = 779,
"C>T" = 588,
"T>A" = 706,
"T>C" = 384,
"T>G" = 127
)
signatures <- simulate_signature_matrix(
signatures = c("sig1", "sig2", "sig3", "sig4"),
channels = c("C>A", "C>G", "C>T", "T>A", "T>C", "T>G"),
seed=1
)
# fitting using nnls method
sig_fit(observed_counts, signatures, method = "nnls")
#> Error in sig_fit(observed_counts, signatures, method = "nnls"): The package "nnls" is required to fit signatures to data when method =
#> nnls