| plotTE {ribosomeProfilingQC} | R Documentation |
Scatterplot of RNA/RPFs level compared to the translational efficiency.
plotTE(
TE,
sample,
xaxis = c("mRNA", "RPFs"),
removeZero = TRUE,
log2 = TRUE,
breaks.length = 50,
...
)
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. |
A invisible data.frame with x, y of points.
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)