R/MutationalPatterns.R

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

# Global package variables

# Default colours for mutation spectrum plotting
COLORS6 <- c(
  "#2EBAED", "#000000", "#DE1C14",
  "#D4D2D2", "#ADCC54", "#F0D0CE"
)

COLORS7 <- c(
  "#2EBAED", "#000000", "#DE1C14",
  "#E98C7B", "#D4D2D2", "#ADCC54",
  "#F0D0CE"
)

SUBSTITUTIONS <- c("C>A", "C>G", "C>T", "T>A", "T>C", "T>G")
SUBSTITUTIONS_96 <- rep(SUBSTITUTIONS, each = 16)
SUBSTITUTIONS_192 <- rep(SUBSTITUTIONS, each = 32)

C_TRIPLETS <- c(
  "ACA", "ACC", "ACG", "ACT",
  "CCA", "CCC", "CCG", "CCT",
  "GCA", "GCC", "GCG", "GCT",
  "TCA", "TCC", "TCG", "TCT"
)

T_TRIPLETS <- c(
  "ATA", "ATC", "ATG", "ATT",
  "CTA", "CTC", "CTG", "CTT",
  "GTA", "GTC", "GTG", "GTT",
  "TTA", "TTC", "TTG", "TTT"
)

CONTEXTS_96 <- c(rep(C_TRIPLETS, 3), rep(T_TRIPLETS, 3))

# combine substitutions and context in one
TRIPLETS_96 <- paste(substr(CONTEXTS_96, 1, 1), "[", SUBSTITUTIONS_96, "]", substr(CONTEXTS_96, 3, 3), sep = "")

STRAND <- rep(c("U", "T"), 96)
DNA_BASES <- c("A", "C", "G", "T")