## ----style, echo = FALSE, results = 'asis'--------------------------------- BiocStyle::markdown(css.files = c('custom.css')) ## ---- echo=FALSE----------------------------------------------------------- suppressPackageStartupMessages( library(tRNAdbImport) ) ## ----eval=FALSE------------------------------------------------------------ # library(tRNAdbImport) ## -------------------------------------------------------------------------- # accessing tRNAdb # tRNA from yeast for Alanine and Phenylalanine gr <- import.tRNAdb(organism = "Saccharomyces cerevisiae", aminoacids = c("Phe","Ala")) ## -------------------------------------------------------------------------- # get a Phenylalanine tRNA from yeast gr <- import.tRNAdb.id(tdbID = gr[gr$tRNA_type == "Phe",][1]$tRNAdb_ID) ## -------------------------------------------------------------------------- # find the same tRNA via blast gr <- import.tRNAdb.blast(blastSeq = gr$tRNA_seq) ## -------------------------------------------------------------------------- # accessing mtRNAdb # get the mitochrondrial tRNA for Alanine in Bos taurus gr <- import.mttRNAdb(organism = "Bos taurus", aminoacids = "Ala") ## -------------------------------------------------------------------------- # get one mitochrondrial tRNA in Bos taurus. gr <- import.mttRNAdb.id(mtdbID = gr[1]$tRNAdb_ID) ## -------------------------------------------------------------------------- # check that the result has the appropriate columns istRNAdbGRanges(gr) ## ---- echo=FALSE----------------------------------------------------------- suppressPackageStartupMessages({ library(Biostrings) library(rtracklayer) }) ## -------------------------------------------------------------------------- library(Biostrings) library(rtracklayer) writeXStringSet(gr$tRNA_seq, filepath = tempfile()) gff <- tRNAdb2GFF(gr) export.gff3(gff, con = tempfile()) ## -------------------------------------------------------------------------- sessionInfo()