plotTE: Plot translational efficiency

In ribosomeProfilingQC: Ribosome Profiling Quality Control

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)

ribosomeProfilingQC documentation built on March 13, 2021, 2:01 a.m.