plotQLDisp
From edgeR v3.14.0
by Yunshun Chen
Plot the quasilikelihood dispersion
Plot the genewise quasilikelihood dispersion against the gene abundance (in log2 counts per million).
 Keywords
 plot
Usage
plotQLDisp(glmfit, xlab="Average Log2 CPM", ylab="QuarterRoot Mean Deviance", pch=16, cex=0.2, col.shrunk="red", col.trend="blue", col.raw="black", ...)
Arguments
 glmfit
 a
DGEGLM
object produced byglmQLFit
.  xlab
 label for the xaxis.
 ylab
 label for the yaxis.
 pch
 the plotting symbol. See
points
for more details.  cex
 plot symbol expansion factor. See
points
for more details.  col.shrunk
 color of the points representing the shrunk quasiliklihood dispersions.
 col.trend
 color of line showing dispersion trend.
 col.raw
 color of points showing the unshrunk dispersions.
 ...
 any other arguments are passed to
plot
.
Details
This function displays the quarterroot of the quasilikelihood dispersions for all genes, before and after shrinkage towards a trend.
If glmfit
was constructed without an abundance trend, the function instead plots a horizontal line (of colour col.trend
) at the common value towards which dispersions are shrunk.
The quarterroot transformation is applied to improve visibility for dispersions around unity.
Value

A plot is created on the current graphics device.
Examples
nbdisp < 1/rchisq(1000, df=10)
y < DGEList(matrix(rnbinom(6000, size = 1/nbdisp, mu = 10),1000,6))
design < model.matrix(~factor(c(1,1,1,2,2,2)))
y < estimateDisp(y, design)
fit < glmQLFit(y, design)
plotQLDisp(fit)
fit < glmQLFit(y, design, abundance.trend=FALSE)
plotQLDisp(fit)
Community examples
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