strandPlot {ribosomeProfilingQC} | R Documentation

## 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"), ...)

### Arguments

`reads` | Output of getPsiteCoordinates
`CDS` | Output of prepareCDS
`col` | Coloar for sense and antisense strand.
`...` | 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)

[Package ribosomeProfilingQC version 1.2.1 Index]