Description Usage Arguments Value Objects from the Class Slots Methods Warning Author(s) See Also Examples
The SuperCurveSettings class represents the arguments needed to perform curve fitting.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | 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,
...)
|
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 |
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 |
antibodyfile |
character string specifying filename containing mapping
from quantification files to antibodies, or |
software |
character string specifying the software used to generate
the quantification files (see section ‘Details’ of
|
alt.layout |
character string specifying the name of the alternative
layout to be used (see section ‘Details’ of |
monitor |
object of (sub)class |
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 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
.
Although objects of the class can be created by a direct call to
new, the preferred method is to use the
SuperCurveSettings
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
: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
signature(object = "SuperCurveSettings")
:
Returns string representation of object.
signature(object = "SuperCurveSettings")
:
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 proebuck@mdanderson.org
Directory
,
RPPADesignParams
,
RPPASpatialParams
,
RPPAFitParams
,
RPPANormalizationParams
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## 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)
|
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