sc98-SuperCurveSettings-class: Class "SuperCurveSettings"

In SuperCurve: RPPA Analysis Package

Description

The SuperCurveSettings class represents the arguments needed to perform curve fitting.

Usage

SuperCurveSettings(txtdir,
                   imgdir,
                   outdir,
                   designparams,
                   fitparams,
                   spatialparams=NULL,
                   normparams,
                   doprefitqc=FALSE,
                   onlynormqcgood=doprefitqc,
                   antibodyfile=NULL,
                   software=NULL,
                   alt.layout=NULL)
fitCurveAndSummarizeFromSettings(settings, monitor=NULL)
is.SuperCurveSettings(x)
## S4 method for signature 'SuperCurveSettings'
write.summary(object,
              path=as(object@outdir, "character"),
              ...)
## S4 method for signature 'SuperCurveSettings'
paramString(object,
            designparams.slots,
            fitparams.slots,
            spatialparams.slots,
            normparams.slots,
            ...)

Arguments

txtdir	character string specifying the directory containing quantification files in text format
imgdir	character string specifying the directory containing TIFF image files associated with each of the aforementioned quantification files, or NULL
outdir	character string specifying the directory where output from analysis should be stored. Must be writable.
designparams	object of class RPPADesignParams
fitparams	object of class RPPAFitParams
spatialparams	object of class RPPASpatialParams, or NULL
normparams	object of class RPPANormalizationParams
doprefitqc	logical scalar. If TRUE, performs pre-fit quality control.
onlynormqcgood	logical scalar. If TRUE, filters the slides to be normalized according to their pre-fit quality control scores.
antibodyfile	character string specifying filename containing mapping from quantification files to antibodies, or NULL
software	character string specifying the software used to generate the quantification files (see section ‘Details’ of RPPA), or NULL to use the default value.
alt.layout	character string specifying the name of the alternative layout to be used (see section ‘Details’ of RPPA), or NULL to use the implicit layout.)
monitor	object of (sub)class ProgressMonitor, or NULL
object	object of class SuperCurveSettings
settings	object of class SuperCurveSettings
x	object of class SuperCurveSettings
path	character string specifying the directory where settings summary should be saved. Must be writable.
designparams.slots	strings specifying RPPADesignParams slotnames to display (for debugging)
fitparams.slots	strings specifying RPPAFitParams slotnames to display (for debugging)
spatialparams.slots	strings specifying RPPASpatialParams slotnames to display (for debugging)
normparams.slots	strings specifying RPPANormalizationParams slotnames to display (for debugging)
...	extra arguments for generic routines

Value

The SuperCurveSettings generator returns an object of class SuperCurveSettings.

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

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

The write.summary method invisibly returns NULL.

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 SuperCurveSettings generator function.

Slots

txtdir:

object of class Directory specifying the directory containing quantification files in text format

imgdir:

object of class Directory specifying the directory containing TIFF image files

outdir:

object of class Directory specifying the directory where analysis results should be stored

designparams:

object of class RPPADesignParams specifying the parameters that describe how a particular set of RPPA slides was designed

fitparams:

object of class RPPAFitParams specifying the parameters that control model fit

spatialparams:

object of class RPPASpatialParams specifying the parameters that control spatial adjustment

normparams:

object of class RPPANormalizationParams specifying the parameters that control normalization

doprefitqc:

logical scalar specifying whether to perform pre-fit quality control

onlynormqcgood:

logical scalar specifying whether to filter the slides to be normalized according to their pre-fit quality control scores

antibodyfile:

character string specifying filename containing mapping from quantification files to antibodies, or NULL

software:

character string specifying the software used to generate the quantification files, or NULL

alt.layout:

character string specifying the name of the alternative layout to be used, or NULL

version:

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

Methods

paramString

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

write.summary

signature(object = "SuperCurveSettings"):
Writes a text file representation of object.

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)

P. Roebuck [e-mail]

See Also

Directory, RPPADesignParams, RPPASpatialParams, RPPAFitParams, RPPANormalizationParams

Examples

  ## Not run: 
extdata.dir <- system.file("extdata", package="SuperCurveSampleData")

txtdir <- file.path(extdata.dir, "rppaTumorData")
designparams <- RPPADesignParams(center=FALSE,
                                 controls=list("neg con", "pos con"),
                                 grouping="blockSample")
fitparams <- RPPAFitParams(ignoreNegative=FALSE,
                           measure="Mean.Total",
                           method="nlrob",
                           model="loess",
                           warnLevel=-1)
normparams <- RPPANormalizationParams(method="median")
settings <- SuperCurveSettings(txtdir=txtdir,
                               imgdir=NULL,
                               outdir=tempdir(),
                               designparams=designparams,
                               spatialparams=NULL,
                               fitparams=fitparams,
                               normparams=normparams)
fitCurveAndSummarizeFromSettings(settings)
  
## End(Not run)

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