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

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## 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

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

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