metaPlot {ribosomeProfilingQC} | R Documentation |
Plot the average coverage of UTR5, CDS and UTR3.
metaPlot( UTR5coverage, CDScoverage, UTR3coverage, sample, xaxis = c("RPFs", "mRNA"), bins = c(UTR5 = 100, CDS = 500, UTR3 = 100), ... )
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. |
A list contain the data for plot.
## 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)