Signature renormalisation

Transform a signature into what it would look like if called from a different pipeline/genome/organism to account for the different 'mutation opportunites'

Usage

sig_renormalise(signature, opportunities_original, opportunities_new)

Arguments

signature

sigverse style signature data.frames. See sigshared::example_signature().

opportunities_original

named vector of mutation opportunities for each context. See sig_opportunities().

opportunities_new

named vector of mutation opportunities for each context. See sig_opportunities().

Value

sigverse style signature data.frame. See sigshared::example_signature().

Examples

opps <- sig_opportunities()
signature <- data.frame(
  channel = c("A[C>G]G", "A[C>G]C", "A[C>G]T"),
  type = c("C>G", "C>G", "C>G"),
  fraction = c(0.4, 0.1, 0.5)
)

# Convert genome signature to panel signature (TSO 500)
sig_renormalise(
  signature,
  opps$GRCh38_genome_trinucleotide_autosomal,
  opps$GRCh38_tso500_trincucleotide_autosomal
)
#>   channel type   fraction
#> 1 A[C>G]G  C>G 0.62127379
#> 2 A[C>G]C  C>G 0.08744164
#> 3 A[C>G]T  C>G 0.29128457