get_sig_exposure: Get Signature Exposure from 'Signature' Object

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Get Signature Exposure from 'Signature' Object

Description

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'.

Usage

get_sig_exposure(
  Signature,
  type = c("absolute", "relative"),
  rel_threshold = 0.01
)

Arguments

Signature	a Signature object obtained either from sig_extract or sig_auto_extract, or just a raw exposure matrix with column representing samples (patients) and row representing signatures.
type	'absolute' for signature exposure and 'relative' for signature relative exposure.
rel_threshold	only used when type is 'relative', relative exposure less than (<=) this value will be set to 0 and thus all signature exposures may not sum to 1. This is similar to this argument in sig_fit.

Value

a data.table

Author(s)

Shixiang Wang [e-mail]

References

Kim, Jaegil, et al. "Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors." Nature genetics 48.6 (2016): 600.

Examples

# 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

sigminer documentation built on May 29, 2024, 3:11 a.m.