RPPA-class {RPPASPACE}

Class “RPPA”

Description

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

Usage

RPPA(file,
     path=".",
     slideNumber=NA,
     antibody=NULL,
     tracking=NULL,
     seriesToIgnore=NULL,
	 warningsFileName="warnings.txt"
	 )
is.RPPA(x)
## S4 method for signature 'RPPA'
dim(x)
## S4 method for signature 'RPPA'
image(x, measure="Net.Value", 
     main = .mkPlotTitle(measure,
                 x@antibody),
     colorbar=FALSE, col=terrain.colors(256), ...)
## S4 method for signature 'RPPA'
summary(object, ...)
seriesNames(rppa)
seriesToUseToMakeCurve(rppa)

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.

slideNumber

integer containing the index of the slide currently being processed.

warningsFileName

character string holding the name of the file to which to write out warning messages generated during processing.

tracking

data.frame used to track the points data from a slide and how they are used. (see section ‘Tracking’ below)

seriesToIgnore

Comma separated list of series names to ignore. These series will not be used to calculate the curve used to fit data. Names in list must match series names in sample file.

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.

...

extra arguments for generic or plotting routines

rppa

object of class RPPA

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 14 columns of information:

Order	Spot number order in file
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
Series.Id	unique numeric identifier of sample spotted at location
Spot.Type	type of spot at location
Dilution	measurement representing background-corrected mean intensity of the spot
Net.Value	measurement representing background-corrected mean intensity of the spot
Raw.Value	measurement representing mean intensity of the spot
Background.Value	measurement representing mean background intensity of the spot
Spot.X.Position	X location of spot on graphic image
Spot.Y.Position	Y location of spot on graphic image
Original.Order	Spot number order in original input file

Taken together, the four components (Main.Row, Sub.Row, Main.Col, Sub.Col) give the logical location of aspot on an array. Additional columns may be included.

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.

The seriesNames function returns a character vector containing the names of the unique (non-control) dilution series on the array.

The seriesToUseToMakeCurve function returns a character vector containing the names of the unique (non-control) dilution series on the array that are used to create a curve to fit samples to.

Tracking

An object for tracking how points in the slide are to be used in the process. The information comes from the sample file of the first slide that has a valid layout. The layout of all other slides are compared to this and skipped if they don't have an identical layout.

Slots

spotType	Spot.Type according to design file.	No default
isNegCtrl	Is point a Negative Control Point.	Default: FALSE	TRUE if value of Spot.Type is negative control type (Blank, Buffer, NegCtrl)
isPosCtrl	Is point a Positive Control Point.	Default: FALSE	TRUE if value of Spot.Type is positive control type (PosCtrl, or PosCtrl-Noise)
isCtrl	Is point a Control Point.	Default: FALSE	TRUE if value of Spot.Type is any control type (Blank, Buffer, NegCtrl, PosCtrl or PosCtrl-Noise)
applySpatialCorrection	Apply spatial correction to point	Default: TRUE	FALSE if Spot.Type in design file is any control type, but TRUE if an Noise type.
makePartOfCurve	Should point be used to create curve to which to fit data?	Default: TRUE	FALSE if SpotType is control type or noise type (Blank, Buffer, Noise, NegCtrl, PosCtrl or PosCtrl-Noise) or in SeriesToIgnore parameter
fitToCurve	Should point be fit to curve?	Default: TRUE	FALSE if point is control in design but not a noise point (Blank, Buffer, NegCtrl, or PosCtrl)
isNoise	Should point be used in noise calculations	Default: FALSE	TRUE if Noise Point (Noise or PosCtrl-Noise)
isSample	Is point a sample point?	Default: TRUE	FALSE if not Sample Point in design file
badPoint	Does this point have a value that was not used or caused problems in processing and whos output accuracy should be questioned?	Default: FALSE	Used as status indicator during run.
dilution	Dilution value for this point. (Decimal value from slide).

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

slideNumber:

integer containing the index of the slide currently being processed.

antibody

character string specifying name of antibody

tracking

data.frame used to track the points data from a slide and how they are used. (see section ‘Tracking’ below)

seriesToIgnore

NULL or Comma separated list of series names to ignore. These series will not be used to calculate the curve used to fit data. Names in list must match series names in sample file.

warningsFileName

character string holding the name of the file to which to write out warning messages generated during processing.

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.

Author(s)

Kevin R. Coombes [e-mail], P. Roebuck [e-mail], James M. Melott [e-mail]

See Also

RPPADesignParams, RPPAFit