metaPlot {ribosomeProfilingQC} | R Documentation

## Metagene analysis plot

### Description

Plot the average coverage of UTR5, CDS and UTR3.

### Usage

    metaPlot(
      UTR5coverage,
      CDScoverage,
      UTR3coverage,
      sample,
      xaxis = c("RPFs", "mRNA"),
      bins = c(UTR5 = 100, CDS = 500, UTR3 = 100),
      ...
    )

### Arguments

`UTR5coverage, CDScoverage, UTR3coverage` | Coverages of UTR5, CDS, and UTR3 region. Output of coverageDepth
`sample` | character(1). Sample name to plot.
`xaxis` | What to plot for x-axis.
`bins` | Bins for UTR5, CDS and UTR3.
`...` | Parameter pass to plot.

### Value

A list contain the data for plot.

### Examples

    ## Not run:
    path <- system.file("extdata", package="ribosomeProfilingQC")
    RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE)
    RNAs <- dir(path, "mRNA.*?\\.[12].bam$", full.names=TRUE)
    gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
    cvgs <- coverageDepth(RPFs[1], RNAs[1], gtf)
    cvgs.utr3 <- coverageDepth(RPFs[1], RNAs[1], gtf, region="utr3")
    cvgs.utr5 <- coverageDepth(RPFs[1], RNAs[1], gtf, region="utr5")
    metaPlot(cvgs.utr5, cvgs, cvgs.utr3, sample=1)

    ## End(Not run)

[Package ribosomeProfilingQC version 1.4.0 Index]