## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ---- echo=FALSE, message = FALSE--------------------------------------------- url <- paste0("https://raw.githubusercontent.com/Koohoko/Koohoko.github.io/", "master/SynMut/images/component.png") ## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("BiocManager")) # install.packages("BiocManager") # if (!requireNamespace("SynMut")) # BiocManager::install("SynMut") ## ---- message=FALSE----------------------------------------------------------- library("SynMut") filepath.fasta <- system.file("extdata", "example.fasta", package = "SynMut") filepath.csv <- system.file("extdata", "target_regions.csv", package = "SynMut") region <- read.csv(filepath.csv) ## ----------------------------------------------------------------------------- rgd.seq <- input_seq(filepath.fasta, region) rgd.seq ## ----------------------------------------------------------------------------- get_dna(rgd.seq) ## ----------------------------------------------------------------------------- str(get_region(rgd.seq)) get_region(input_seq(filepath.fasta)) ## ----------------------------------------------------------------------------- get_cu(rgd.seq) get_du(rgd.seq) get_nu(rgd.seq) ## ----------------------------------------------------------------------------- # Random synonymous mutations mut.seq <- codon_random(rgd.seq) # Compare the codon usage get_cu(mut.seq) - get_cu(rgd.seq) # Keeping the original codon usage pattern mut.seq <- codon_random(rgd.seq, keep = TRUE) # Compare the codon usage get_cu(mut.seq) - get_cu(rgd.seq) ## ----------------------------------------------------------------------------- # Fifty percent of the codons were allowed for mutation mut.seq <- codon_random(rgd.seq, n = 0.5) # Compare the codon usage get_cu(mut.seq) - get_cu(rgd.seq) ## ----------------------------------------------------------------------------- # Generate AAC-maximized mutations mut.seq <- codon_to(rgd.seq, max.codon = "AAC") # Compare the codon usage get_cu(mut.seq) - get_cu(rgd.seq) # Generate AAC-minimized mutations mut.seq <- codon_to(rgd.seq, min.codon = "AAC") # Compare the codon usage get_cu(mut.seq) - get_cu(rgd.seq) ## ----------------------------------------------------------------------------- # Maximaize the usage of "CG" dinucleotide in the pre-defined region mut.seq <- dinu_to(rgd.seq, max.dinu = "cg") # Check the dinucelotide usage difference between the mutant and the original get_du(mut.seq) - get_du(rgd.seq) # Minimize the usage of "CA", and compare the dinucleotide usage. mut.seq <- dinu_to(rgd.seq, min.dinu = "CA") get_du(mut.seq) - get_du(rgd.seq) # Maximize the usage of "CG" while keeping the original codon usage mut.seq <- dinu_to(rgd.seq, max.dinu = "cg", keep = TRUE) # Compare the dinucleotide usage get_du(mut.seq) - get_du(rgd.seq) # Compare the codon usage get_cu(mut.seq) - get_cu(rgd.seq) ## ----------------------------------------------------------------------------- # Use a codon usage vector as a target target <- get_cu(rgd.seq)[2,] mut.seq <- codon_mimic(rgd.seq, alt = target) # Compare the codon usage get_cu(mut.seq) - get_cu(rgd.seq) # Use a sequence as a target target <- Biostrings::DNAStringSet("TTGAAAA-CTC-N--AAG") mut.seq <- codon_mimic(rgd.seq, alt = target) # Compare the codon usage get_cu(mut.seq) - get_cu(rgd.seq) # Compare the synonymous codon usage frequency get_freq(mut.seq) - get_freq(rgd.seq) # Compare the Relative Synonymous Codon Usage (RSCU) get_rscu(mut.seq) - get_rscu(rgd.seq) ## ---- eval = FALSE------------------------------------------------------------ # Biostrings::writeXStringSet(get_dna(rgd.seq), "rgd.fasta") ## ----------------------------------------------------------------------------- sessionInfo()