RPPASPACESettings-class {RPPASPACE}

Class “RPPASPACESettings”

Description

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

Usage

RPPASPACESettings(txtdir,
				imgdir,
				outdir,
				designparams,
				fitparams,
				spatialparams=NULL,
				normparams,
				doprefitqc=FALSE,
				onlynormqcgood=doprefitqc,
				parallelClusterSize=as.integer(1),
				createcombinedoutputimage = FALSE,
				imageextension=".tif", 
				imagerotation=as.integer(0),
				residualsrotation=as.integer(0),
				warningsFileName="warnings.txt",
				errorsFileName = "errors.txt"
)
fitCurveAndSummarizeFromSettings(settings)
is.RPPASPACESettings(x)
## S4 method for signature 'RPPASPACESettings'
write.summary(object,
              path=as(object@outdir, "character"),
              ...)
## S4 method for signature 'RPPASPACESettings'
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 image files associated with each of the aforementioned quantification files, or NULL. All image files for a given run must be of one image file type. Other files in the directory will be ignored.

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.

parallelClusterSize

Number of parallel cpus to use on computer when running RPPASPACE. Spatial corrections and fitting diltion series to the calculated curve sections of the code will be done in parallel when this number is greater than 1. Defaults to 1 for backwards compatibility if not specified.

createcombinedoutputimage

logical scalar. If TRUE, an output png file will be created for each valid slide in the set. The png file that is a composite of the two generated png files and the original slide image.

imageextension

character string specifying extension to use when searching for images matching the slide file names. Acceptable values are (".tif", ".png", ".bmp", ".gif", ".jpg")

imagerotation

numeric scalar containing 90 degree value to rotate the input image by when appending it below the generated graphs in the combined output image file for each slide. Defaults to 0 if not specified. Acceptable values (0, 90, 180, 270)

residualsrotation

numeric scalar containing 90 degree value to rotate the generated residuals image by when generating the output graphic. This should be used if the layout of the information in the input txt file does not match the orientation of the slide input image. Defaults to 0 if not specified. Acceptable values (0, 90, 180, 270)

warningsFileName

character string specifying file to append any warnings generated by this function. Defaults to "warnings.txt"

errorsFileName

character string specifying file to append any errors generated by this function. Defaults to "errors.txt"

object

object of class RPPASPACESettings

settings

object of class RPPASPACESettings

x

object of class RPPASPACESettings

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 RPPASPACESettings generator returns an object of class RPPASPACESettings.

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

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 RPPASPACESettings 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:

see argument

createcombinedoutputimage:

see argument

imageextension:

see argument

imagerotation:

see argument

residualsrotation:

see argument

onlynormqcgood:

see argument

seriesToIgnore:

see argument

parallelClusterSize:

see argument

warningsFileName:

see argument

errorsFileName:

see argument

Methods

paramString

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

write.summary

signature(object = "RPPASPACESettings"):
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], James M. Melott [e-mail]

See Also

Directory, RPPADesignParams, RPPASpatialParams, RPPAFitParams, RPPANormalizationParams

Examples

    ## Not run: 
showClass("RPPASPACESettings")

#Insert an existing directory containing txt, img, and out subdirectories
#
analysishome <- "C:/temp"  

txtdir <- file.path(analysishome, "txt" )
imgdir <- file.path(analysishome, "img" )
outdir <- file.path(analysishome, "out")
number_cpus_to_use <- 2

warningsFileName <- "warnings.txt"
errorsFileName <- "errors.txt"

designparams <- RPPADesignParams(center=FALSE,
							seriesToIgnore=list(),
							majorXDivisions=as.integer(10),
							majorYDivisions=as.integer(10)
							)

spatialparams <- RPPASpatialParams(cutoff=0.8,
							k=100,
							gamma=0.1,
							plotSurface=FALSE)

fitparams <- RPPAFitParams(measure="Net.Value",
							method="nls",
							model="cobs",
							trim=2,
							ci=FALSE,
							ignoreNegative=FALSE,
							warnLevel=-1
							)

normparams <- RPPANormalizationParams(method="none")

settings <- RPPASPACESettings(txtdir=txtdir,
				imgdir=imgdir,
				outdir=outdir,
				designparams=designparams,
				spatialparams=spatialparams,
				doprefitqc=TRUE,
				fitparams=fitparams,
				normparams=normparams,
				onlynormqcgood=FALSE,
				imageextension=".jpg",
				createcombinedoutputimage=TRUE,
				warningsFileName=warningsFileName,
				parallelClusterSize=as.integer(number_cpus_to_use))

#Print the created object
paramString(settings)
	
## End(Not run)