Barplot of PM and MM Intensities for Device

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Description

Creates a barplot of mean perfect match and mismatch intensities for the selected device.

Usage

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plotPM(x,
       which   = "",
       size    = 0,
       transfo = NULL,
       method  = mean,
       names   = "namepart",
       beside  = TRUE,
       col     = c("red", "blue"),
       legend  = c("PM","MM"),
       las     = 2,
       ylab    = "mean intensities",
       dev     = "screen",
       outfile = "PMPlot",
       w       = 540,
       h       = 540,
       ...) 

Arguments

x

object of class DataTreeSet.

which

type of probes to be used, for details see validData.

size

length of sequence to be generated as subset.

transfo

a valid function to transform the data, usually “log2”, or “0”.

method

method to compute average intensities, “mean” or “median”.

names

optional vector of sample names.

beside

logical. If FALSE, mean intensities are portrayed as stacked bars, and if TRUE the columns are portrayed as juxtaposed bars.

col

color of PM, MM bars.

legend

a vector of text used to construct a legend for the plot, or a logical indicating whether a legend should be included.

las

the style of axis labels.

ylab

a title for the y axis.

dev

graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.

outfile

the name of the output file.

w

the width of the device in pixels.

h

the height of the device in pixels.

...

optional arguments to be passed to barplot.

Details

Produces barplots of mean perfect match and mismatch intensities for slot data for an object of class DataTreeSet.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as pmplot.

Author(s)

Christian Stratowa

See Also

pmplot

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