2021-11-16 05:31:48 +00:00
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gen_mutations <- function(seq, N) {
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sealKey() # See: http://steipe.biochemistry.utoronto.ca/abc/index.php/BCH441_Code_submisson_instructions
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stats <- c()
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stats <- cbind(stats, c(0, 0, 0))
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rownames(stats) <- c("silent", "missense", "nonsense")
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colnames(stats) <- c("occurrences")
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# Actual function
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for (i in 1:N) {
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original_seq <- Biostrings::DNAString(seq)
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aa_seq <- Biostrings::translate(original_seq, no.init.codon = TRUE)
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mut_seq <- Biostrings::DNAString(seq)
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mut_index <- sample(1:length(original_seq), 1, replace = TRUE)
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possible_mutations <- Biostrings::DNA_BASES
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possible_mutations <- possible_mutations[possible_mutations != as.character(unlist(original_seq[mut_index]))]
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mut_seq <- Biostrings::replaceLetterAt(mut_seq, mut_index, sample(possible_mutations, 1, replace = TRUE))
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mut_aa <- Biostrings::translate(mut_seq, no.init.codon = TRUE)
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term_aa <- regexpr(pattern = "\\*", aa_seq)
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term_mut_aa <- as.integer(regexpr(pattern = "\\*", mut_aa))
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if ((term_aa == -1 && term_mut_aa != -1) || (term_mut_aa != -1 && term_mut_aa < term_aa)) {
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stats["nonsense", "occurrences"] <- 1 + stats["nonsense", "occurrences"]
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} else if (mut_aa == aa_seq) {
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stats["silent", "occurrences"] <- 1 + stats["silent", "occurrences"]
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} else {
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stats["missense", "occurrences"] <- 1 + stats["missense", "occurrences"]
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}
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}
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sealKey()
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return(stats)
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}
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gen_mutations("ATGATGATGATGATGATG", 1000)
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gen_mutations("CCCCCCCCCCCCCCCCCC", 500)
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gen_mutations("TATTACTATTACTATTAC", 500)
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gen_mutations("TGGTGGTGGTGGTGGTGGTGGTGG", 500)
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gen_mutations("TGTTGTTGTTGTTGTTGTTGTTGT", 500)
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gen_mutations("TGTTGTTGTTGTTGTTGTTGTTGA", 500)
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myFA <- readFASTA("data/RAB39B_HSa_coding.fa")
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myFA <- rbind(myFA, readFASTA("data/PTPN5_HSa_coding.fa"))
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myFA <- rbind(myFA, readFASTA("data/PTPN11_HSa_coding.fa"))
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myFA <- rbind(myFA, readFASTA("data/KRAS_HSa_coding.fa"))
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rownames(myFA)<-c("RAB39B", "PTPN5", "PTPN11", "KRAS") # Assign row names
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gen_mutations(myFA["RAB39B", 2], 10000)
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gen_mutations(myFA["PTPN5", 2], 10000)
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gen_mutations(myFA["PTPN11", 2], 10000)
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gen_mutations(myFA["KRAS", 2], 10000)
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