plotProbeset: Plot of Probe Intensities for a Probeset for Device.
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Note Author(s) See Also

Creates a line plot of probe intensities for a probeset for the selected device.

plotProbeset(x,
             unitID,
             unittype   = "transcript",
             which      = "pm",
             transfo    = log2,
             names      = "namepart",
             ylim       = NULL,
             col        = 1:6,
             lty        = 1:5,
             add.legend = FALSE,
             dev        = "screen",
             outfile    = "ProbesetPlot",
             w          = 540,
             h          = 540,
             ...)

`x`	object of class `DataTreeSet`.
`unitID`	unit ID of probeset with type of ID determined by parameter `unittype`.
`unittype`	`character` vector, one of “unit”, “transcript”, “probeset”.
`which`	type of probes to be used, for details see `validData`.
`transfo`	a valid function to transform the data, usually “log2”, or “0”.
`names`	optional vector of sample names.
`ylim`	range for the plotted y values.
`col`	color to use for the different samples.
`lty`	line types to use for the different samples.
`add.legend`	logical, if TRUE a legend of sample names will be drawn. Optionally, a character indicating the position of the legend, default is “topleft”.
`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 `plotProbeset`.

Produces line plots of the probe intensities for probeset unitID. Probe intensities are taken from slot data.

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, line plots of probe intensities will only be drawn for these columns.

Data must first be attached to class DataTreeSet using method attachInten. Furthermore, unit names must be attached using method attachUnitNames.

Christian Stratowa

probesetplot

xps documentation built on Nov. 8, 2020, 6 p.m.