## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html ) ## ----vignetteSetup, echo=FALSE, message=FALSE, warning=FALSE------------------ ## Track time spent on making the vignette startTime <- Sys.time() ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle")[1], knitr = citation("knitr")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], sessioninfo = citation("sessioninfo")[1], testthat = citation("testthat")[1], txcutr = citation("txcutr")[1] ) ## ----"install", eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("txcutr") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----"citation"--------------------------------------------------------------- ## Citation info citation("txcutr") ## ----"txdb_sgd", message=FALSE------------------------------------------------ library(GenomicFeatures) library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene) txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene ## constrain to "chrI" seqlevels(txdb) <- "chrI" ## view the lengths of first ten transcripts transcriptLengths(txdb)[1:10,] ## ----"truncate_sgd"----------------------------------------------------------- library(txcutr) txdb_w500 <- truncateTxome(txdb, maxTxLength=500) transcriptLengths(txdb_w500)[1:10,] ## ----"export_gtf", eval=FALSE------------------------------------------------- # gtf_file <- tempfile("sacCer3_chrI.sgd.txcutr_w500", fileext=".gtf.gz") # exportGTF(txdb_w500, file=gtf_file) ## ----"export_fasta", eval=FALSE----------------------------------------------- # library(BSgenome.Scerevisiae.UCSC.sacCer3) # sacCer3 <- BSgenome.Scerevisiae.UCSC.sacCer3 # # fasta_file <- tempfile("sacCer3_chrI.sgd.txcutr_w500", fileext=".fa.gz") # exportFASTA(txdb_w500, genome=sacCer3, file=fasta_file) ## ----"merge_table"------------------------------------------------------------ df_merge <- generateMergeTable(txdb_w500, minDistance=500) head(df_merge, 10) ## ----"merged_txs"------------------------------------------------------------- df_merge[df_merge$tx_in != df_merge$tx_out,] ## ----------------------------------------------------------------------------- transcripts(txdb_w500, columns=c("tx_name", "gene_id"), filter=list(gene_id=c("YAL026C"))) ## ----createVignette, eval=FALSE----------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("intro.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("intro.Rmd", tangle = TRUE) ## ----reproduce1, echo=FALSE--------------------------------------------------- ## Date the vignette was generated Sys.time() ## ----reproduce2, echo=FALSE--------------------------------------------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits = 3) ## ----reproduce3, echo=FALSE------------------------------------------------------------------------------------------- ## Session info library("sessioninfo") options(width = 120) session_info() ## ----vignetteBiblio, results = "asis", echo = FALSE, warning = FALSE, message = FALSE--------------------------------- ## Print bibliography PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))