data-raw/build_deconstructSigs_stuff.R

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

# The 96 trinuc-context-specific SNVs, in the order used by deconstructSigs data structures
# Note that the central reference trinucleotides are always C/T, as A/G reference are 
# represented using the reverse complement trinucleotide context
build_deconstructSigs_trinuc_string = function() {
	return(c("A[C>A]A",
	  		 "A[C>A]C",
	  		 "A[C>A]G",
	  		 "A[C>A]T",
	  		 "C[C>A]A",
	  		 "C[C>A]C",
	  		 "C[C>A]G",
	  		 "C[C>A]T",
	  		 "G[C>A]A",
	  		 "G[C>A]C",
	  		 "G[C>A]G",
	  		 "G[C>A]T",
	  		 "T[C>A]A",
	  		 "T[C>A]C",
	  		 "T[C>A]G",
	  		 "T[C>A]T",
	  		 "A[C>G]A",
	  		 "A[C>G]C",
	  		 "A[C>G]G",
	  		 "A[C>G]T",
	  		 "C[C>G]A",
	  		 "C[C>G]C",
	  		 "C[C>G]G",
	  		 "C[C>G]T",
	  		 "G[C>G]A",
	  		 "G[C>G]C",
	  		 "G[C>G]G",
	  		 "G[C>G]T",
	  		 "T[C>G]A",
	  		 "T[C>G]C",
	  		 "T[C>G]G",
	  		 "T[C>G]T",
	  		 "A[C>T]A",
	  		 "A[C>T]C",
	  		 "A[C>T]G",
	  		 "A[C>T]T",
	  		 "C[C>T]A",
	  		 "C[C>T]C",
	  		 "C[C>T]G",
	  		 "C[C>T]T",
	  		 "G[C>T]A",
	  		 "G[C>T]C",
	  		 "G[C>T]G",
	  		 "G[C>T]T",
	  		 "T[C>T]A",
	  		 "T[C>T]C",
	  		 "T[C>T]G",
	  		 "T[C>T]T",
	  		 "A[T>A]A",
	  		 "A[T>A]C",
	  		 "A[T>A]G",
	  		 "A[T>A]T",
	  		 "C[T>A]A",
	  		 "C[T>A]C",
	  		 "C[T>A]G",
	  		 "C[T>A]T",
	  		 "G[T>A]A",
	  		 "G[T>A]C",
	  		 "G[T>A]G",
	  		 "G[T>A]T",
	  		 "T[T>A]A",
	  		 "T[T>A]C",
	  		 "T[T>A]G",
	  		 "T[T>A]T",
	  		 "A[T>C]A",
	  		 "A[T>C]C",
	  		 "A[T>C]G",
	  		 "A[T>C]T",
	  		 "C[T>C]A",
	  		 "C[T>C]C",
	  		 "C[T>C]G",
	  		 "C[T>C]T",
	  		 "G[T>C]A",
	  		 "G[T>C]C",
	  		 "G[T>C]G",
	  		 "G[T>C]T",
	  		 "T[T>C]A",
	  		 "T[T>C]C",
	  		 "T[T>C]G",
	  		 "T[T>C]T",
	  		 "A[T>G]A",
	  		 "A[T>G]C",
	  		 "A[T>G]G",
	  		 "A[T>G]T",
	  		 "C[T>G]A",
	  		 "C[T>G]C",
	  		 "C[T>G]G",
	  		 "C[T>G]T",
	  		 "G[T>G]A",
	  		 "G[T>G]C",
	  		 "G[T>G]G",
	  		 "G[T>G]T",
	  		 "T[T>G]A",
	  		 "T[T>G]C",
	  		 "T[T>G]G",
	  		 "T[T>G]T"))
}

# data table with context (e.g., A), central mutation (e.g., G), and corresponding deconstructSigs notation (G[C>G]C)
build_dS_notation_table = function() {
  dt = data.table::fread(system.file("extdata/trinuc_snv_to_deconstructSigs_ID.txt", package = "cancereffectsizeR"))
  setkey(dt, "context", "mutation")
  return(dt)
}