The expected number of mutations (or copy number segment records) with each signature was determined after a scaling transformation V ~ WH = W'H' where W' = WU' and H' = UH. The scaling matrix U is a KxK diagnal matrix (K is signature number, U' is the inverse of U) with the element corresponding to the L1-norm of column vectors of W (ie. the sum of the elements of the vector). As a result, the k-th row vector of the final matrix H' represents the absolute exposure (activity) of the k-th process across samples (e.g., for SBS, the estimated (or expected) number of mutations generated by the k-th process). Of note, for copy number signatures, only components of feature CN was used for calculating H'.
get_sig_exposure( Signature, type = c("absolute", "relative"), rel_threshold = 0.01 )
'absolute' for signature exposure and 'relative' for signature relative exposure.
only used when type is 'relative', relative exposure less
Kim, Jaegil, et al. "Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors." Nature genetics 48.6 (2016): 600.
Shixiang Wang firstname.lastname@example.org
# Load mutational signature load(system.file("extdata", "toy_mutational_signature.RData", package = "sigminer", mustWork = TRUE )) # Get signature exposure expo1 <- get_sig_exposure(sig2) expo1 expo2 <- get_sig_exposure(sig2, type = "relative") expo2