readsDistribution: Plot reads distribution in genomic elements

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Plot reads distribution in genomic elements

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,
  precedence = NULL,
  ignore.seqlevelsStyle = FALSE,
  ...
)

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
precedence	If no precedence specified, double count will be enabled, which means that if the reads overlap with both CDS and 5'UTR, both CDS and 5'UTR will be incremented. If a precedence order is specified, for example, if promoter is specified before 5'UTR, then only promoter will be incremented for the same example. The values could be any combinations of "CDS", "UTR5", "UTR3", "OtherExon", "Intron", "upstream", "downstreama" and "InterGenic", Default=NULL
ignore.seqlevelsStyle	Ignore the sequence name style detection 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)
pc.sub <- readsDistribution(pc.sub, txdb, las=2,
              precedence=c(
              "CDS", "UTR5", "UTR3", "OtherExon",
              "Intron", "upstream", "downstream",
              "InterGenic"
              ))

jianhong/ribosomeProfilingQC documentation built on Nov. 3, 2024, 6:33 p.m.