Class “RPPASpatialParams”

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Description

The RPPASpatialParams class is used to bundle the parameter set together that control how to perform spatial adjustment into a reusable object.

Usage

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RPPASpatialParams(cutoff=0.8,
                  k=100,
                  gamma=0.1,
                  plotSurface=FALSE)
is.RPPASpatialParams(x)
## S4 method for signature 'RPPASpatialParams'
paramString(object, slots, ...)

Arguments

cutoff

numeric scalar used to identify the background cutoff with value in closed interval [0..1]. Default is 0.8.

k

numeric scalar used as smoothing model argument. Default is 100.

gamma

numeric scalar used as model parameter with value in closed interval [0..2]. Default is 0.1.

plotSurface

logical scalar. If TRUE, plots surfaces. Default is FALSE.

object

object of class RPPASpatialParams

x

object of class RPPASpatialParams

slots

strings specifying RPPASpatialParams slotnames to display (for debugging)

...

extra arguments for generic routines

Details

The cutoff argument passed to quantile is percentile of the background estimates used to define the noise region of slide.

The k argument passed to s sets upper limit on degrees of freedom associated with smoothing.

The gamma argument passed to gam provides a constant multiplier used to inflate model degrees of freedom in the GCV or UBRE/AIC score.

Value

The RPPASpatialParams generator returns an object of class RPPASpatialParams.

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

The paramString method returns a character vector, possibly empty but never 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 RPPASpatialParams generator function.

Slots

cutoff:

numeric scalar; see arguments above

k:

numeric scalar; see arguments above

gamma:

numeric scalar; see arguments above

plotSurface:

logical scalar; see arguments above

Methods

paramString(object)

Returns string 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 proebuck@mdanderson.org

See Also

spatialCorrection

Examples

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showClass("RPPASpatialParams")
spatialparams <- RPPASpatialParams()
paramString(spatialparams)

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