Description Usage Arguments Details Value Objects from the Class Slots Methods Note Author(s) See Also Examples
The RPPA class represents the raw quantification data from a reverse-phase protein array experiment.
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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 |
antibody |
character string specifying antibody name. If missing,
default value is filename (referenced by |
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 |
x |
object of class |
measure |
character string containing the name of the measurement column
in |
main |
character string used to title the image plot |
colorbar |
logical scalar that determines whether to include a
color bar in the plot. If |
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 |
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.
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.
Although objects of the class can be created by a direct call to
new, the preferred method is to use the
RPPA
generator function.
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
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.
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")
Kevin R. Coombes kcoombes@mdanderson.org, P. Roebuck proebuck@mdanderson.org
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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)
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