RPPASet-class: Class “RPPASet”

Description

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

Usage

RPPASet(path,
        designparams,
        fitparams,
        spatialparams=NULL,
        normparams,
        doprefitqc=FALSE,
	    parallelClusterSize,
		residualsrotation = as.integer(0),
	    warningsFileName="warnings.txt",
	    printTimings=TRUE
)
is.RPPASet(x)
# S4 method for RPPASet
normalize(object,
          ...)
# S4 method for RPPASet
summary(object,
        onlynormqcgood=ran.prefitqc(object),
        ...)
# S4 method for RPPASet
write.summary(object,
              path,
              prefix="rppaspace",
              graphs=TRUE,
			  createcombinedoutputimage=FALSE,
              imagedir=NULL,
              onlynormqcgood=ran.prefitqc(object),
              imageextension=".tif",
              imagerotation=as.integer(0),
              residualsrotation=as.integer(0),
			  majorXDivisions = object@design@majorXDivisions, 
			  majorYDivisions = object@design@majorYDivisions,
              ...)

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.

Arguments

path: character string specifying a directory. In the case of the RPPASet generator, it specifies the directory containing the quantification files (.txt) 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 rppaspace 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.
printTimings: TRUE/FALSE whether or not to print out the time taken as the method is run. Used for performance debugging purposes.
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.
createcombinedoutputimage: logical scalar. If TRUE, produces output png consisting of combined png images and scaled version of original slide image.
imagedir: character string specifying the directory containing the images corresponding to the quantification files
imageextension: character string specifying extension to use when searching for images matching the slide file names.
imagerotation: numeric scalar containing 90 degree value to rotate the input image by when appending it to the generated graphs in the combined output image file for each slide.
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.
majorXDivisions: integer to describe distance between grid lines on the X axis of the R2 residuals plot. Defaults to 10 if NA or invalid value provided.
majorYDivisions: integer to describe distance between grid lines on the Y axis of the R2 residuals plot. Defaults to 10 if NA or invalid value provided.
warningsFileName: character string specifying file to append any warnings generated by this function.
onlynormqcgood: logical scalar. If TRUE, filters the slides to be normalized according to their pre-fit quality control scores.
x: object of class RPPASet
parallelClusterSize: Number of parallel cores to use when processing.
...: extra arguments for generic or plotting routines

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 RPPADesignParams, common to all the slides
errorsFileName:: character string holding the name of the file to which to write out error messages generated during processing.
warningsFileName:: character string holding the name of the file to which to write out warning messages generated during processing.
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

Kevin R. Coombes coombes.3@osu.edu, P. Roebuck paul_roebuck@comcast.net, James M. Melott jmmelott@mdanderson.org

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.

Potentially generates multiple CSV and TSV files: one for the raw concentrations (rppaspace_conc_raw.csv"), one for the \(R^2\) statistics (rppaspace_ss_ratio.csv), and one for the normalized concentrations (rppaspace_conc_norm_[norm_method].csv); a fourth file containing the goodness of fit probabilities (rppaspace_prefit_qc.csv) may be present if pre-fit QC analysis was requested. If spatial adjustments were requested, a TSV file (spatial_adjustments.tsv) will be created. If positive control dilution series have been declared as Noise or PosCtrl-Noise points in the design file, an additional CSV file of noise statistics will be created (rppaspace_noise.csv). If prefit QC analysis was done and/or noise qc metric were created, a combined qc metrics file will be created (rppaspace_combined_qc.csv) as well. Additionally, a TSV file detailing completion of each stage of processing for each slide is produced (rppaspace_summary.tsv).

If imagedir 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 original slide image is merged with these output PNG graph files, generating an additional JPEG file per antibody.