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## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown(css.files = c('custom.css')) ## ----echo=FALSE--------------------------------------------------------------- suppressPackageStartupMessages({ library(tRNAscanImport) }) ## ----------------------------------------------------------------------------- library(tRNAscanImport) yeast_file <- system.file("extdata", file = "yeast.tRNAscan", package = "tRNAscanImport") # output for sacCer3 # Before readLines(con = yeast_file, n = 7L) ## ----------------------------------------------------------------------------- # output for sacCer3 # After gr <- import.tRNAscanAsGRanges(yeast_file) head(gr, 2) # Any GRanges passing this, can be used for subsequent function istRNAscanGRanges(gr) ## ----echo=FALSE--------------------------------------------------------------- suppressPackageStartupMessages({ library(Biostrings) library(rtracklayer) }) ## ----------------------------------------------------------------------------- library(Biostrings) library(rtracklayer) # suppressMessages(library(rtracklayer, quietly = TRUE)) # Save tRNA sequences writeXStringSet(gr$tRNA_seq, filepath = tempfile()) # to be GFF3 compliant use tRNAscan2GFF gff <- tRNAscan2GFF(gr) export.gff3(gff, con = tempfile()) ## ----------------------------------------------------------------------------- # tRNAscan-SE output for hg38 human_file <- system.file("extdata", file = "human.tRNAscan", package = "tRNAscanImport") # tRNAscan-SE output for E. coli MG1655 eco_file <- system.file("extdata", file = "ecoli.tRNAscan", package = "tRNAscanImport") # import tRNAscan-SE files gr_human <- import.tRNAscanAsGRanges(human_file) gr_eco <- import.tRNAscanAsGRanges(eco_file) # get summary plots grl <- GRangesList(Sce = gr, Hsa = gr_human, Eco = gr_eco) plots <- gettRNAFeaturePlots(grl) ## ----plot1, fig.cap = "tRNA length."------------------------------------------ plots$length ## ----plot2, fig.cap = "tRNAscan-SE scores."----------------------------------- plots$tRNAscan_score ## ----plot3, fig.cap = "tRNA GC content."-------------------------------------- plots$gc ## ----plot4, fig.cap = "tRNAs with introns."----------------------------------- plots$tRNAscan_intron ## ----plot5, fig.cap = "Length of the variable loop."-------------------------- plots$variableLoop_length ## ----echo=FALSE--------------------------------------------------------------- suppressPackageStartupMessages({ library(BSgenome.Scerevisiae.UCSC.sacCer3) }) ## ----tRNA_precursor----------------------------------------------------------- library(BSgenome.Scerevisiae.UCSC.sacCer3) genome <- getSeq(BSgenome.Scerevisiae.UCSC.sacCer3) # renaming chromosome to match tRNAscan output names(genome) <- c(names(genome)[-17L],"chrmt") tRNAprecursor <- get.tRNAprecursor(gr, genome) head(tRNAprecursor) ## ----------------------------------------------------------------------------- sessionInfo()