RPPA-class {SuperCurve}R Documentation

The RPPA Class

Description

The RPPA class represents the raw quantification data from a reverse-phase protein array experiment.

Usage

RPPA(filename, path = ".")
## S4 method for signature 'RPPA':
summary(object, ...)
## S4 method for signature 'RPPA':
image(x, measure = "Mean.Net", main = measure, colorbar
= FALSE, col = terrain.colors(256), ...)

Arguments

filename The name of a file containing MicroVigene quantifications of a reverse-phase protein array experiment.
path An optional argument giving the path from the current directory to the file. The default value assumes the file is contained in the current direectory.
object An RPPA object.
x An RPPA object.
measure A character string containing the name of the measurement column in data that should be displayed by the image method.
main A character string used to title the image plot
colorbar A logical value that determines whether to include a color bar in the plot. Default is FALSE.
col The usual graphics parameter used by image. It is included here to change the default color scheme to use terrain.colors.
... The usual extra arguments for generic or plotting routines.

Details

The data frame slot (data) in a valid RPPA object constructed from a MicroVigene input file using the RPPA function is guaranteed to contain at least 6 columns of information: Main.Row, Main.Col, Sub.Row, Sub.Col, Sample, and Mean.Net. The first four pieces of information give the logical location of a spot on an array, after which we get a unique identifier of the sample spotted at that location and a measurement that represents the background-corrected mean intensity of the spot. Additional columns may be included or may be added later.

Value

The RPPA constructor returns an object of the RPPA class.
The summary method returns a summary of the underlying data frame.
The image method invisibly returns the RPPA object on which it was invoked.

Objects from the Class

Although objects of the class can be created by a direct call to new, the preferred method is to use the RPPA function.

Slots

data:
A data.frame containing the contents of a MicroVigene or other quantification file
file:
A character string: the name of the file that the data was loaded from

Methods

summary(object, ...)
The summary method prints a summary of the underlying data frame.
image(x, measure="Mean.Net", main=measure, colorbar=FALSE, col=terrain.colors(256), ...)
The image method produces a "geographic" image of the measurement column named by the measure argument. The colors in the image represent the intensity of the measurement at each spot on the array, and the display locations match the row and column locations of the spot. Any measurement column can be displayed using this function. An optional color bar can be added; this will be placed at the right edge.

Author(s)

Kevin R. Coombes <kcoombes@mdanderson.org>

References

KRC

See Also

RPPAFit, RPPADesign

Examples

path <- system.file("rppaTumorData", package="SuperCurve")
erk2 <- RPPA("ERK2.txt", path=path)
summary(erk2)
image(erk2)
image(erk2, colorbar=TRUE)
image(erk2, "Vol.Bkg", main="Background Estimates", colorbar=TRUE)
[Package SuperCurve version 0.931 Index]