volcanoPlot.BMEA: Draw a volcano plot from a BMEA array
In steveped/BMEA: Bayesian Modelling for Exon Arrays

Description Usage Arguments Details See Also

Draws a volcano plot incorporating the possiblity of points with an infinite value on the y-axis.

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volcanoPlot.BMEA(data, plotVal = "mean", cont = 1, hLight = NULL,
  hLightCol = "blue", hLight.lab.cex = 0.7, hLight.pt.cex = 1,
  hLight.n = 10, pch = 16, cex = 0.35, main, ...)

`data`	the results from analysis with the BMEA model. Can be an `AffymetrixCelSetList`, `array` or `matrix`
`plotVal`	determines which summary statistic to plot. Defaults to mean, but can also accept median or any other saved summary statistic named in the array
`cont`	determines which contrast to plot. Equates to the the third dimension of any BmeaArray provided
`hLight`	specify any points to be highlighted by unit ID
`hLightCol`	the colour to use when highlighting points
`hLight.lab.cex`	the scaling factor for point labelling
`hLight.pt.cex`	the scaling factor to use when highlighting points
`hLight.n`	the number of points to highlight
`pch`	see `plot`
`cex`	see `plot`
`main`	see `title`
`...`	any further parameters to be passed to `plot`

Will draw a volcano plot from the results. Only a single contrast can be plotted, and any requested points will be highlighted, up to the maximum specified by hLight.n

extractBmeaArray

steveped/BMEA documentation built on May 30, 2019, 5:38 p.m.