plotBCV: Plot Biological Coefficient of Variation

Description Usage Arguments Details Value Author(s) Examples

View source: R/plotBCV.R

Description

Plot the genewise biological coefficient of variation (BCV) against gene abundance (in log2 counts per million).

Usage

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plotBCV(y, xlab="Average log CPM", ylab="Biological coefficient of variation",
     pch=16, cex=0.2, col.common="red", col.trend="blue", col.tagwise="black", ...)

Arguments

y

a DGEList object.

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.common

color of line showing common dispersion

col.trend

color of line showing dispersion trend

col.tagwise

color of points showing genewise dispersions. Note that ‘tag’ and ‘gene’ are synonymous here.

...

any other arguments are passed to plot.

Details

The BCV is the square root of the negative binomial dispersion. This function displays the common, trended and genewise BCV estimates.

Value

A plot is created on the current graphics device.

Author(s)

Davis McCarthy, Yunshun Chen, Gordon Smyth

Examples

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BCV.true <- 0.1
y <- DGEList(matrix(rnbinom(6000, size = 1/BCV.true^2, mu = 10),1000,6))
y <- estimateCommonDisp(y)
y <- estimateTrendedDisp(y)
y <- estimateTagwiseDisp(y)
plotBCV(y)

Example output

Loading required package: limma

edgeR documentation built on Nov. 1, 2018, 4:13 a.m.