strandPlot: Plot the distribution of reads in sense and antisense strand

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Plot the distribution of reads in sense and antisense strand

Description

Plot the distribution of reads in sense and antisense strand to check the mapping is correct.

Usage

strandPlot(
  reads,
  CDS,
  col = c("#009E73", "#D55E00"),
  ignore.seqlevelsStyle = FALSE,
  ...
)

Arguments

reads	Output of getPsiteCoordinates
CDS	Output of prepareCDS
col	Coloar for sense and antisense strand.
ignore.seqlevelsStyle	Ignore the sequence name style detection or not.
...	Parameter passed to barplot

Value

A ggplot object.

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)
CDS <- prepareCDS(txdb)
strandPlot(pc.sub, CDS)

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