plotMA: MA-plot from base means and log fold changes

Description Usage Arguments Details See Also Examples

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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