plotTE {ribosomeProfilingQC}R Documentation

Plot translational efficiency

Description

Scatterplot of RNA/RPFs level compared to the translational efficiency.

Usage

plotTE(
  TE,
  sample,
  xaxis = c("mRNA", "RPFs"),
  removeZero = TRUE,
  log2 = TRUE,
  breaks.length = 50,
  ...
)

Arguments

TE

Output of translationalEfficiency

sample

character(1). Sample name to plot.

xaxis

What to plot for x-axis.

removeZero

Remove the 0 values from plots.

log2

Do log2 transform or not.

breaks.length

Length of breaks for histogram.

...

Parameters pass to plot.

Value

A invisible data.frame with x, y of points.

Examples

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")
#cnts <- countReads(RPFs, RNAs, gtf, level="gene")
cnts <- readRDS(file.path(path, "cnts.rds"))
fpkm <- getFPKM(cnts)
te <- translationalEfficiency(fpkm)
plotTE(te, 1)

[Package ribosomeProfilingQC version 1.6.0 Index]