plotQLDisp

From edgeR v3.14.0 by Yunshun Chen

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.

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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