## ---- include = FALSE----------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) options(width = 70) ## ----setup---------------------------------------------------------- library(eisaR) ## ------------------------------------------------------------------- gtf <- system.file("extdata/gencode.v28.annotation.sub.gtf", package = "eisaR") grl <- getFeatureRanges( gtf = gtf, featureType = c("spliced", "intron"), intronType = "separate", flankLength = 50L, joinOverlappingIntrons = FALSE, verbose = TRUE ) ## ------------------------------------------------------------------- grl ## ------------------------------------------------------------------- lapply(S4Vectors::metadata(grl)$featurelist, head) ## ------------------------------------------------------------------- head(S4Vectors::metadata(grl)$corrgene) ## ------------------------------------------------------------------- suppressPackageStartupMessages({ library(BSgenome) library(BSgenome.Hsapiens.UCSC.hg38) }) seqs <- GenomicFeatures::extractTranscriptSeqs( x = BSgenome.Hsapiens.UCSC.hg38, transcripts = grl ) seqs ## ------------------------------------------------------------------- exportToGtf( grl, filepath = file.path(tempdir(), "exported.gtf") ) ## ------------------------------------------------------------------- df <- getTx2Gene(grl) head(df) tail(df) ## ------------------------------------------------------------------- sessionInfo()