probesetplot-methods: Plot of Probe Intensities for a Probeset.

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Creates a line plot of probe intensities for a probeset.

Usage

probesetplot(x, unitID, unittype = "transcript", which = "pm", transfo = log2, names = "namepart", ylim = NULL, col = 1:6, lty = 1:5, add.legend = FALSE, ...)

Arguments

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”.
...	optional arguments to be passed to probesetplot.

Details

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.

Note

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

Author(s)

Christian Stratowa

See Also

plotPM, boxplot, barplot

Examples

## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## need to attach probe intensities and optionally unit names
data.test3 <- attachUnitNames(data.test3)
data.test3 <- attachInten(data.test3)

if (interactive()) {
probesetplot(data.test3, unitID="100084_at", unittype="transcript", add.legend=TRUE)
}

## optionally remove unit names and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeUnitNames(data.test3)

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