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Finished mutation generator.

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Harrison Deng 2021-11-01 11:23:18 -04:00
parent a5c1c80549
commit b1e00f52f7
1 changed files with 54 additions and 0 deletions
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myScripts/ABC-INT-Mutation_impact-code.R Normal file
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myFA <- readFASTA("data/RAB39B_HSa_coding.fa")
myFA <- rbind(myFA, readFASTA("data/PTPN5_HSa_coding.fa"))
myFA <- rbind(myFA, readFASTA("data/PTPN11_HSa_coding.fa"))
myFA <- rbind(myFA, readFASTA("data/KRAS_HSa_coding.fa"))
rownames(myFA)<-c("RAB39B", "PTPN5", "PTPN11", "KRAS") # Assign row names
gen_mutations <- function(seq, N) {
stats <- c()
stats <- cbind(stats, c(0, 0, 0))
rownames(stats) <- c("silent", "missense", "nonsense")
colnames(stats) <- c("occurrences")
# Actual function
for (i in 1:217) {
# select index for mutation
working_seq <- Biostrings::DNAString(seq)
aa_seq <- Biostrings::translate(working_seq, no.init.codon = TRUE)
mut_action <- sample(c("ins", "del", "sub"), 1, TRUE)
mut_seq <- Biostrings::DNAString(seq)
if (mut_action == "sub") {
mut_index <- sample(1:length(working_seq), 1, replace = TRUE)
possible_mutations <- Biostrings::DNA_BASES
possible_mutations <- possible_mutations[possible_mutations != as.character(unlist(working_seq[mut_index]))]
mut_change <- sample(possible_mutations, 1, replace = TRUE)
mut_seq <- Biostrings::replaceLetterAt(mut_seq, mut_index, mut_change)
} else if (mut_action == "ins") {
mut_index <- sample(1:length(working_seq) - 2, 1, replace = TRUE)
possible_mutations <- Biostrings::DNA_BASES
mut_seq <- Biostrings::DNAString(paste(substring(working_seq, 1, mut_index - 1), sample(possible_mutations, 1), substring(working_seq, mut_index), sep = ""))
} else {
mut_index <- sample(1:length(working_seq), 1, replace = TRUE)
mut_seq <- mut_seq[-mut_index]
}
mut_seq <- Biostrings::DNAString(substring(mut_seq, 1, length(mut_seq) - (length(mut_seq) %% 3)))
mut_aa <- Biostrings::translate(mut_seq, no.init.codon = TRUE)
# Note: we need silent, nonsense, and missense
mut_aa_stop <- match("*", Biostrings::as.matrix(mut_aa))
aa_seq_stop <- match("*", Biostrings::as.matrix(aa_seq))
if (!is.na(mut_aa_stop) & (is.na(aa_seq_stop) | mut_aa_stop < aa_seq_stop)) {
stats["nonsense", "occurrences"] <- 1 + stats["nonsense", "occurrences"]
} else if (mut_aa == aa_seq) {
stats["silent", "occurrences"] <- 1 + stats["silent", "occurrences"]
} else {
stats["missense", "occurrences"] <- 1 + stats["missense", "occurrences"]
}
}
return(stats)
}
N_test <- 1200
gen_mutations("ATGATGATGATGATGATG", N_test)
gen_mutations("CCCCCCCCCCCCCCCCCC", N_test)
gen_mutations("TATTACTATTACTATTAC", N_test)
gen_mutations("TGGTGGTGGTGGTGGTGGTGGTGG", N_test)
gen_mutations("TGTTGTTGTTGTTGTTGTTGTTGT", N_test)