plotBCV {edgeR} | R Documentation

## Plot Biological Coefficient of Variation

### Description

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

### Usage

    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

    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)

[Package edgeR version 3.24.3 Index]