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# 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")
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