sc02-RPPADesign-class: Class "RPPADesign" and Class "RPPADesignParams"

In SuperCurve: RPPA Analysis Package

Description

The RPPADesign class represents the information that describes how a particular set of RPPA slides was designed. The RPPADesignParams class is used to bundle the parameter set together for easier re-use.

Usage

RPPADesign(raw,
           steps=rep(0, 1),
           series=factor(rep(0, 1)),
           grouping=c("byRow","byCol", "bySample", "blockSample"),
           ordering=c("decreasing","increasing"),
           alias=NULL,
           center=FALSE,
           controls=NULL,
           aliasfile=NULL,
           designfile=NULL,
           path=".")

RPPADesignParams(steps=rep(0,1),
                 series=factor(rep(0,1)),
                 grouping=c("byRow", "byCol", "bySample", "blockSample"),
                 ordering=c("decreasing", "increasing"),
                 alias=NULL,
                 center=FALSE,
                 controls=NULL,
                 aliasfile=NULL,
                 designfile=NULL,
                 path=".")

RPPADesignFromParams(raw, designparams)

getSteps(design)
is.RPPADesign(x)
is.RPPADesignParams(x)
seriesNames(design)
## S4 method for signature 'RPPADesign'
dim(x)
## S4 method for signature 'RPPADesign'
image(x, main, ...)
## S4 method for signature 'RPPADesign'
names(x)
## S4 method for signature 'RPPADesignParams'
paramString(object, slots, ...)
## S4 method for signature 'RPPA,RPPADesign'
plot(x, y, measure, main, ...)
## S4 method for signature 'RPPADesign'
summary(object, ...)

Arguments

raw	data frame, matrix, or object of class RPPA.
designparams	object of class RPPADesignParams.
steps	numeric vector listing the dilution step associated with each spot, on a logarithmic scale.
series	character vector or factor identifying the dilution series to which each spot corresponds.
grouping	character string specifying the orientation of the dilution series on the array. Valid values are: "byRow" each row of a subgrid is its own dilution series "byColumn" each column of a subgrid is its own dilution series "bySample" each unique sample id is its own dilution series "blockSample" all occurrences of sample id in subgrid refer to same series
ordering	character string specifying arrangement of dilution series. Valid values are: "decreasing" arranged in order of decreasing concentrations "increasing" arranged in order of increasing concentrations
alias	optional list or data frame for attaching sample labels or biologically relevant descriptors to the dilution series with the following required named components: Alias Label to use in lieu of sample name Sample Sample name to match
aliasfile	optional character string specifying filename. Data would be read by read.delim and expected format is as described above for alias argument.
designfile	optional character string specifying filename. Data would be read by read.delim and expected format is that produced as output by the SlideDesignerGUI package.
path	optional character string specifying directory path to prepend when either aliasfile or designfile argument refer to relative filename; ignored when filename is absolute.
center	logical scalar. If TRUE, then dilution steps are centered around 0.
controls	optional list containing the character strings that identify control spots on the array. RPPADesignParams will also coerce a character vector appropriately.
x	object of class RPPADesign (or RPPA in plot method)
y	object of class RPPADesign
object	object of class RPPADesign (or RPPADesignParams in paramString method)
design	object of class RPPADesign
slots	strings specifying RPPADesignParams slotnames to display (for debugging)
main	overall title for plot
measure	character string specifying measure to plot
...	extra arguments for generic or plotting routines

Details

From their inception, reverse-phase protein array experiments have spotted samples on the array in dilution series. Thus, a critical aspect of the design and analysis is to understand how the dilution series are placed on the array.

The optional grouping and ordering arguments allows the user to specify several standard layouts without having to go into great detail. The most common layout is byRow, which indicates that each row of a subgrid on the array should be considered as a separate dilution series. Although considerably less common (for reasons related to the robotics of how arrays are printed), the byCol layout indicates that each column of a subgrid is its own dilution series. The bySample layout means that each unique sample name indicates its own dilution series. Finally, the blockSample layout indicates that all occurrences of a sample name within a subgrid (or block) refer to the same dilution series. The blockSample layout can be used, for example, when a dilution series is long enough to extend over more than one row of a subgrid. One layout we have seen used seven dilution steps followed by a control spot, contained in two successive rows of a design with 4x4 subgrids, leading to the pattern:

7 6 5 4

3 2 1 C

If the design of an RPPA experiment does not follow one of the built-in patterns, you can create an object by supplying vectors of dilution series names (in the series argument) and corresponding dilution steps (in the steps argument) that explicitly provide the mapping for each spot.

The arguments alias and aliasfile are mutually exclusive; they specify the exact same thing. The arguments controls and designfile are also mutually exclusive. The SampleType column of the slide design datafile is used to automatically populate the controls slot of RPPADesign class.

Value

The RPPADesign generator returns an object of class RPPADesign.

The RPPADesignParams generator returns an object of class RPPADesignParams.

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

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

The dim method returns a numeric vector of length 4.

The image method invisibly returns the displayed matrix of dilution steps.

The names method returns a character vector.

The paramString method returns a character vector, possibly empty but never NULL.

The summary method returns the summary object of the layout data frame.

The getSteps function returns a numeric vector containing, for each non-control spot, the step represented by that spot in its dilution series.

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

Objects from the Class

Although objects of these classes can be created by a direct call to new, the preferred method is to start with the RPPADesignParams generator, followed by the RPPADesignFromParams function to construct the final object (the RPPADesign generator is directly implemented in this way).

Slots

For RPPADesign class:

call:

object of class call specifying the function call that was used during construction

layout:

data frame

alias:

list

sampleMap:

character vector

controls:

list containing character strings that identify control spots on the array. Controls are not included as part of any dilution series.

For RPPADesignParams class:

steps:

see corresponding argument above

series:

see corresponding argument above

grouping:

see corresponding argument above

ordering:

see corresponding argument above

center:

see corresponding argument above

controls:

list or NULL. see corresponding argument above

alias:

list or NULL. see corresponding argument above

aliasfile:

character specifying absolute pathname of file containing alias information, or NULL

designfile:

character specifying absolute pathname of file containing slide design information, or NULL

Methods

dim

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

image

signature(x = "RPPADesign"):
Produces a two-dimensional graphical display of the layout design. Colors are used to represent different dilution steps, and laid out in the same pattern as the rows and columns of the array. This provides a visual check that the design has been specified correctly.

names

signature(x = "RPPADesign"):
Returns the names of the samples on the slide.

paramString

signature(object = "RPPADesignParams"):
Returns string representation of object.

plot

signature(x = "RPPA", y = "RPPADesign"):
Plots an object of class RPPA by showing its dilution series with respect to the corresponding object of class RPPADesign.

summary

signature(object = "RPPADesign"):
Lists the names of the control spots on the array and prints a summary of the data frame describing the layout.

Warning

The paramString method should not be called by user except for informational purposes. The content and format of the returned string may vary between different versions of this package.

Author(s)

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

See Also

RPPA

Examples

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

txtdir <- file.path(extdata.dir, "rppaTumorData")
erk2 <- RPPA("ERK2.txt", path=txtdir)
design <- RPPADesign(erk2, grouping="blockSample", center=TRUE)
dim(design)
image(design)
summary(design)

designparams <- RPPADesignParams(grouping="blockSample",
                                 controls=list("neg con", "pos con"))
design <- RPPADesignFromParams(erk2, designparams)
image(design)
summary(design)

plot(erk2, design)

txtdir <- file.path(extdata.dir, "rppaCellData")
akt <- RPPA("Akt.txt", path=txtdir)
## Uses duplicate 8-step dilution series within 4x4 subgrids.
## They are interleaved, with top two identical rows containing the first
## 4 steps and the bottom two identical rows containing the last 4 steps.
steps <- rep(c(rep(8:5, 2), rep(4:1, 2)), 40) - 4.5
rep.temp <- factor(paste('Rep', rep(rep(1:2, each=4), 80), sep=""))
series <- factor(paste(as.character(akt@data$Sample),
                       as.character(rep.temp),
                       sep="."))
design40 <- RPPADesign(akt, steps=steps, series=series)
dim(design40)
image(design40)
summary(design40)

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