inst/doc/rna-velocity.R

In eisaR: Exon-Intron Split Analysis (EISA) in R

## ---- 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()