sc01-RPPA-class: Class "RPPA"

Description Usage Arguments Details Value Objects from the Class Slots Methods Note Author(s) See Also Examples

Description

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

Usage

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RPPA(file,
     path=".",
     antibody=NULL,
     software="microvigene",
     alt.layout=NULL)
is.RPPA(x)
## S4 method for signature 'RPPA'
dim(x)
## S4 method for signature 'RPPA'
image(x, measure="Mean.Net", main,
      colorbar=FALSE, col=terrain.colors(256), ...)
## S4 method for signature 'RPPA'
summary(object, ...)

Arguments

file

character string or connection specifying text file containing quantifications of a reverse-phase protein array experiment

path

character string specifying the path from the current directory to the file. The default value assumes the file is contained in the current directory. If file is a connection, this argument is ignored.

antibody

character string specifying antibody name. If missing, default value is filename (referenced by file argument) without extension.

software

character string specifying the software used to generate the quantification file (see section ‘Details’ below)

alt.layout

character string specifying the name of the alternative layout to be used (see section ‘Details’ below)

object

object of class RPPA

x

object of class RPPA

measure

character string containing the name of the measurement column in data that should be displayed by the image method

main

character string used to title the image plot

colorbar

logical scalar that determines whether to include a color bar in the plot. If TRUE, the image cannot be used as one panel in a window with multiple plots. Default is FALSE.

col

graphics parameter used by image. It is included here to change the default color scheme to use terrain.colors.

...

extra arguments for generic or plotting routines

Details

The data frame slot (data) in a valid RPPA object constructed from a quantification file using the RPPA generator function is guaranteed to contain at least 6 columns of information:

Main.Row logical location of spot on the array
Main.Col logical location of spot on the array
Sub.Row logical location of spot on the array
Sub.Col logical location of spot on the array
Sample unique identifier of sample spotted at location
Mean.Net measurement representing background-corrected mean intensity of the spot

The first four components (taken together) give the logical location of a spot on an array. Additional columns may be included or added later.

Other methods can be specified to read the quantification files. The software argument is used in the selection of the actual method to perform this function. For example, if the argument value is “foo”, the code will attempt to invoke method read.foo to read the file. The method will be passed a connection object to the file and should return a data frame containing the file's data. The method will be searched for in the global namespace, then within the package itself. The default value selects method read.microvigene, which this package provides to read MicroVigene quantification files in text format. Another method, read.arraypro, is also provided to read Array-Pro quantification files in text format.

Likewise, the logical layout of the slide can also be changed. The alt.layout argument is used in the selection of the actual method to perform this function. For example, if the argument value is “bar”, the code will attempt to invoke method layout.as.bar to convert the physical layout of the data to that specified by the method itself.

Value

The RPPA generator returns an object of class RPPA.

The is.RPPA method returns TRUE if its argument is an object of class RPPA.

The dim method returns a numeric vector of length 4.

The image method invisibly returns the RPPA object on which it was invoked.

The summary method returns a summary of the underlying data frame.

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 generator function.

Slots

data:

data.frame containing the contents of a quantification file

file:

character string specifying the name of the file that the data was loaded from

antibody:

character string specifying name of antibody

Methods

dim

signature(x = "RPPA"):
Returns the dimensions of the slide layout.

image

signature(x = "RPPA"):
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, placed along the right edge.

summary

signature(object = "RPPA"):
Prints a summary of the underlying data frame.

Note

The previous release provided a method, read.singlesubgrid, which could convert a single subgrid physical layout (in MicroVigene format) into its actual logical one.

As this package now supports more than one software package, this had to be reworked! To achieve the same thing in this release, use:
RPPA(file, path, software="microvigene", alt.layout="superslide")

Author(s)

Kevin R. Coombes kcoombes@mdanderson.org, P. Roebuck proebuck@mdanderson.org

See Also

RPPADesign, RPPAFit

Examples

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extdata.dir <- system.file("extdata", package="SuperCurveSampleData")

## Converts file from single subgrid to its logical equivalent (4x12x11x11)
txtdir <- file.path(extdata.dir, "rppaSingleSubgridData")
waldo <- RPPA("Waldo.txt",
              path=txtdir,
              software="microvigene",
              alt.layout="superslide")
dim(waldo)

txtdir <- file.path(extdata.dir, "rppaTumorData")
erk2 <- RPPA("ERK2.txt", path=txtdir)
dim(erk2)
summary(erk2)
image(erk2)
image(erk2, colorbar=TRUE)
image(erk2, "Vol.Bkg", main="Background Estimates", colorbar=TRUE)

SuperCurve documentation built on May 2, 2019, 6:14 p.m.