The RPPA class represents the raw quantification data from a reverse-phase protein array experiment.
RPPA(file,
path=".",
slideNumber=NA,
antibody=NULL,
tracking=NULL,
seriesToIgnore=NULL,
warningsFileName="warnings.txt"
)
is.RPPA(x)
# S4 method for RPPA
dim(x)
# S4 method for RPPA
image(x, measure="Net.Value",
main = .mkPlotTitle(measure,
x@antibody),
colorbar=FALSE, col=terrain.colors(256), ...)
# S4 method for RPPA
summary(object, ...)
seriesNames(rppa)
seriesToUseToMakeCurve(rppa)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.
character string or connection specifying text file containing quantifications of a reverse-phase protein array experiment
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.
character string specifying antibody name. If missing,
default value is filename (referenced by file argument) without
extension.
integer containing the index of the slide currently being processed.
character string holding the name of the file to which to write out warning messages generated during processing.
data.frame used to track the points data from a slide and how they are used. (see section ‘Tracking’ below)
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 of class RPPA
object of class RPPA
character string containing the name of the measurement column
in data that should be displayed by the image method
character string used to title the image plot
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.
graphics parameter used by image.
extra arguments for generic or plotting routines
object of class RPPA
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? |
Although objects of the class can be created by a direct call to
new, the preferred method is to use the
RPPA generator function.
datadata.frame containing the contents of a quantification file
filecharacter string specifying the name of the file that the data was loaded from
slideNumber:integer containing the index of the slide currently being processed.
antibodycharacter string specifying name of antibody
trackingdata.frame used to track the points data from a slide and how they are used. (see section ‘Tracking’ below)
seriesToIgnoreNULL 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.
warningsFileNamecharacter string holding the name of the file to which to write out warning messages generated during processing.
signature(x = "RPPA"):
Returns the dimensions of the slide layout.
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.
signature(object = "RPPA"):
Prints a summary of the underlying data frame.
Kevin R. Coombes coombes.3@osu.edu, P. Roebuck paul_roebuck@comcast.net, James M. Melott jmmelott@mdanderson.org
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.
RPPADesignParams,
RPPAFit