metaPlot: Metagene analysis plot

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

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)

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