plotQLDisp

0th

Percentile

Plot the quasi-likelihood dispersion

Plot the genewise quasi-likelihood dispersion against the gene abundance (in log2 counts per million).

Keywords
plot
Usage
plotQLDisp(glmfit, xlab="Average Log2 CPM", ylab="Quarter-Root Mean Deviance", pch=16, cex=0.2, col.shrunk="red", col.trend="blue", col.raw="black", ...)
Arguments
glmfit
a DGEGLM object produced by glmQLFit.
xlab
label for the x-axis.
ylab
label for the y-axis.
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 quasi-liklihood 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 quarter-root of the quasi-likelihood 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 quarter-root transformation is applied to improve visibility for dispersions around unity.

Value

A plot is created on the current graphics device.

Aliases
  • plotQLDisp
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)
Documentation reproduced from package edgeR, version 3.14.0, License: GPL (>=2)

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