readsDistribution: Plot reads distribution in genomic elements

In ribosomeProfilingQC: Ribosome Profiling Quality Control

Description

Plot the percentage of reads in CDS, 5'UTR, 3'UTR, introns, and other elements.

Usage

readsDistribution(
  reads,
  txdb,
  upstreamRegion = 3000,
  downstreamRegion = 3000,
  plot = TRUE,
  ...
)

Arguments

reads	Output of getPsiteCoordinates
txdb	A TxDb object
upstreamRegion, downstreamRegion	The range for promoter region and downstream region.
plot	Plot the distribution or not
...	Not use.

Value

The reads with distribution assignment

Examples

library(Rsamtools)
bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                           package="ribosomeProfilingQC")
yieldSize <- 10000000
bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
pc <- getPsiteCoordinates(bamfile, bestpsite=11)
pc.sub <- pc[pc$qwidth %in% c(29, 30)]
library(GenomicFeatures)
library(BSgenome.Drerio.UCSC.danRer10)
txdb <- makeTxDbFromGFF(system.file("extdata",
          "Danio_rerio.GRCz10.91.chr1.gtf.gz",
          package="ribosomeProfilingQC"),
          organism = "Danio rerio",
          chrominfo = seqinfo(Drerio)["chr1"],
          taxonomyId = 7955)
pc.sub <- readsDistribution(pc.sub, txdb, las=2)

ribosomeProfilingQC documentation built on March 13, 2021, 2:01 a.m.