plotMA {INSPEcT} | R Documentation

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

### Description

Visualize the comparison between the rates calculated from two different INSPEcT objects profiled in steady-state conditions.

### Usage

    ## S4 method for signature 'INSPEcT_diffsteady'
    plotMA(object, ...)

### Arguments

`object` | An object of calss INSPEcT_diffsteady
`...` | Additional parameters, see Details section

### Details

Possible arguments to "plotMA":

- "rate" - A character, which represent the rate to be visualized, either "synthesis", "processing" or "degradation". By default, "synthesis" is chosen.

- "alpha" - A numeric, The confidence interval for significance (FDR), by default 0.1

- "xlim" - A numeric vector of length 2, limits of x-axis, by default the range of the data.

- "xlab" - A character, the label of x-axis, by default "log2 geometric mean"

- "ylim" - A numeric vector of length 2, limits of y-axis, by default the range of the data.

- "ylab" - A character, the label of y-axis, by default "log2 fold change"

- "main" - A character, the title of the plot, by default the name of the visualized rate.

### See Also

http://en.wikipedia.org/wiki/MA_plot

### Examples

    data('simData3rep', package='INSPEcT')
    data('simData3rep_2', package='INSPEcT')
    diffrates <- compareSteady(simData3rep, simData3rep_2)
    plotMA(diffrates, alpha=.5)

[Package INSPEcT version 1.10.0 Index]