plotQLDisp {edgeR} | R Documentation

## Plot the quasi-likelihood dispersion

### Description

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

### 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 squeezed quasi-likelihood 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.

### Author(s)

Aaron Lun, Davis McCarthy, Gordon Smyth, Yunshun Chen.

### References

Chen Y, Lun ATL, and Smyth, GK (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research 5, 1438. http://f1000research.com/articles/5-1438

### 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)

[Package edgeR version 3.28.1 Index]