RPPASPACESettings-class {RPPASPACE} | R Documentation |
The RPPASPACESettings class represents the arguments needed to perform curve fitting.
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,
...)
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 |
outdir |
character string specifying the directory where output from analysis should be stored. Must be writable. |
designparams |
object of class |
fitparams |
object of class |
spatialparams |
object of class |
normparams |
object of class |
doprefitqc |
logical scalar. If |
onlynormqcgood |
logical scalar. If |
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 |
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 |
settings |
object of class |
x |
object of class |
path |
character string specifying the directory where settings summary should be saved. Must be writable. |
designparams.slots |
strings specifying |
fitparams.slots |
strings specifying |
spatialparams.slots |
strings specifying |
normparams.slots |
strings specifying |
... |
extra arguments for generic routines |
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
.
Although objects of the class can be created by a direct call to
new, the preferred method is to use the
RPPASPACESettings
generator function.
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
signature(object = "RPPASPACESettings")
:
Returns string representation of object.
signature(object = "RPPASPACESettings")
:
Writes a text file representation of object.
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.
P. Roebuck paul_roebuck@comcast.net, James M. Melott jmmelott@mdanderson.org
Directory
,
RPPADesignParams
,
RPPASpatialParams
,
RPPAFitParams
,
RPPANormalizationParams
## 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)