sc11-RPPASet-class: Class "RPPASet"

In SuperCurve: RPPA Analysis Package

Description

The RPPASet class fits supercurves to an entire directory of reverse-phase protein array experiments.

Usage

RPPASet(path,
        designparams,
        fitparams,
        spatialparams=NULL,
        normparams,
        doprefitqc=FALSE,
        monitor=SCProgressMonitor(),
        antibodyfile=NULL,
        software="microvigene",
        alt.layout=NULL)
is.RPPASet(x)
## S4 method for signature 'RPPASet'
normalize(object,
          ...)
## S4 method for signature 'RPPASet'
summary(object,
        onlynormqcgood=ran.prefitqc(object),
        ...)
## S4 method for signature 'RPPASet'
write.summary(object,
              path,
              prefix="supercurve",
              graphs=TRUE,
              tiffdir=NULL,
              onlynormqcgood=ran.prefitqc(object),
              monitor=NULL,
              ...)

Arguments

path	character string specifying a directory. In the case of the RPPASet generator, it specifies the directory containing the quantification files to be processed. In the case of the write.summary method, it specifies the directory where output should be stored.
designparams	object of class RPPADesignParams describing features common to all quantification files
fitparams	object of class RPPAFitParams containing parameters used to fit the supercurve model
spatialparams	object of class RPPASpatialParams containing parameters used to perform spatial adjustment, or NULL
normparams	object of class RPPANormParams containing parameters used to normalize the concentrations
doprefitqc	logical scalar. If TRUE, performs pre-fit quality control.
monitor	object of (sub)class ProgressMonitor
antibodyfile	character string specifying filename containing mapping from quantification files to antibodies
software	character string specifying the software used to generate the quantification file (see section ‘Details’ of RPPA)
alt.layout	character string specifying the name of the alternative layout to be used (see section ‘Details’ of RPPA)
object	object of class RPPASet
prefix	character string used as a filename prefix on files generated by the write.summary method.
graphs	logical scalar. If TRUE, produces fit graphs.
tiffdir	character string specifying the directory containing the TIFF images corresponding to the quantification files
onlynormqcgood	logical scalar. If TRUE, filters the slides to be normalized according to their pre-fit quality control scores.
x	object of class RPPASet
...	extra arguments for generic or plotting routines

Details

Quantify all the slides in a directory using RPPASet generator. This returns an object containing slide data and fits for each slide. Typically this is followed by a call to write.summary to write the resulting quantifications and diagnostic plots to a directory.

The write.summary method (indirectly) generates three CSV files: one for the raw concentrations, one for the R^2 statistics, and one for the normalized concentrations. If tiffdir is NULL, the directory is assumed to be a sibling directory to path named "tif". If graphs is TRUE, two PNG files containing output graphs are created per antibody. The ImageMagick ‘convert’ binary is then used to merge these output graphs with the source TIFF files, generating an additional JPEG file per antibody.

Value

The RPPASet generator returns an object of class RPPASet.

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

The summary method returns an object of class RPPASetSummary.

The write.summary method invisibly returns NULL.

Objects from the Class

Although objects of the class can (in theory) be created by a direct call to new, the only realistic method is to use the RPPASet generator function.

Slots

call:

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

version:

character string containing the version of this package used to construct the object

design:

object of class RPPADesign, common to all the slides

rppas:

array of objects of class RPPA

spatialparams

object of class RPPASpatialParams that was used to perform spatial adjustment, or NULL

prefitqcs:

array of objects of class RPPAPreFitQCParams

fitparams:

object of class RPPAFitParams that was used to construct the model fits

normparams:

object of class RPPANormalizationParams used to normalize the raw concentrations

fits:

array of fitted objects of class RPPAFit

completed:

logical matrix specifying stage completion for each slide

Methods

normalize

signature(object = "RPPASet"):
Assembles matrix of concentrations from all fits in object, using the object's normalization settings.

summary

signature(object = "RPPASet"):
Creates an object of class RPPASetSummary.

write.summary

signature(object = "RPPASet"):
Writes a record of the entire RPPASet, including fitted values, residuals, and images of the processed slides.

Author(s)

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

See Also

RPPA, RPPADesign, RPPAFit, RPPASetSummary, SCProgressMonitor

Examples

  ## Not run: 
parentdir <- file.path("C:", "MyData")
txtdir <- file.path(parentdir, "txt")     # quantification files
imgdir <- file.path(parentdir, "tif")     # and corresponding image files
outdir <- file.path(parentdir, "results") # output files

designparams <- RPPADesignParams(grouping="blockSample",
                                 center=FALSE,
                                 aliasfile="layoutInfo.tsv",
                                 designfile="slidedesign.tsv")
fitparams <- RPPAFitParams(measure="Mean.Net",
                           method="nlrob",
                           model="cobs",
                           ignoreNegative=FALSE,
                           warnLevel=-1,
                           verbose=FALSE)
normparams <- RPPANormalizationParams(method="vs")
monitor <- SCProgressMonitor()
rppaset <- RPPASet(txtdir,
                   designparams,
                   fitparams,
                   normparams=normparams,
                   monitor=monitor)
write.summary(rppaset,
              path=outdir,
              graphs=TRUE,
              tiffdir=imgdir,
              monitor=monitor)
  
## End(Not run)

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