plotMA {DEGreport} | R Documentation

## MA-plot from base means and log fold changes

### Description

MA-plot addaptation to show the shrinking effect.

### Usage

    ## S4 method for signature 'DEGSet'
    plotMA(object, title = NULL, label_points = NULL,
      label_column = "symbol", limit = NULL, diff = 5, raw = FALSE,
      correlation = FALSE, ...)

### Arguments

`object` | DEGSet class.
`title` | Optional. Plot title.
`label_points` | Optionally label these particular points.
`label_column` | Match label_points to this column in the results.
`limit` | Absolute maximum to plot on the log2FoldChange.
`diff` | Minimum difference between logFoldChange before and after shrinking.
`raw` | Whether to plot just the unshrunken log2FC.
`correlation` | Whether to plot the correlation of the two logFCs.
`...` | Optional parameters to pass.

### Value

MA-plot ggplot.

### Author(s)

Victor Barrera

Rory Kirchner

Lorena Pantano

### Examples

    library(DESeq2)
    dds <- makeExampleDESeqDataSet(betaSD=1)
    dds <- DESeq(dds)
    res <- degComps(dds, contrast = list("condition_B_vs_A"))
    plotMA(res[["condition_B_vs_A"]])

[Package DEGreport version 1.16.0 Index]