plsda classification

Classification using the partial least square distcriminant analysis algorithm.

Usage

plsdaClassification(
  object,
  assessRes,
  scores = c("prediction", "all", "none"),
  ncomp,
  fcol = "markers",
  ...
)

Arguments

object

An instance of class "MSnSet".

assessRes

An instance of class "GenRegRes", as generated by plsdaOptimisation.

scores

One of "prediction", "all" or "none" to report the score for the predicted class only, for all classes or none.

ncomp

If assessRes is missing, a ncomp must be provided.

fcol

The feature meta-data containing marker definitions. Default is markers.

...

Additional parameters passed to plsda from package caret.

Value

An instance of class "MSnSet" with plsda and plsda.scores feature variables storing the classification results and scores respectively.

Author

Laurent Gatto

Examples

# \donttest{
## not running this one for time considerations
library(pRolocdata)
data(dunkley2006)
## reducing parameter search space and iterations 
params <- plsdaOptimisation(dunkley2006, ncomp = c(3, 10),  times = 2)
#> 
  |                                                                            
  |                                                                      |   0%
#> Error: package klaR is required
params
#> new("standardGeneric", .Data = function (x, ...) 
#> standardGeneric("params"), generic = "params", package = "S4Vectors", 
#>     group = list(), valueClass = character(0), signature = "x", 
#>     default = NULL, skeleton = (function (x, ...) 
#>     stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
#>         "params"), domain = NA))(x, ...))
#> <bytecode: 0x55cd603bb8f8>
#> <environment: 0x55cd603b7300>
#> attr(,"generic")
#> [1] "params"
#> attr(,"generic")attr(,"package")
#> [1] "S4Vectors"
#> attr(,"package")
#> [1] "S4Vectors"
#> attr(,"group")
#> list()
#> attr(,"valueClass")
#> character(0)
#> attr(,"signature")
#> [1] "x"
#> attr(,"default")
#> `\001NULL\001`
#> attr(,"skeleton")
#> (function (x, ...) 
#> stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
#>     "params"), domain = NA))(x, ...)
#> attr(,"class")
#> [1] "standardGeneric"
#> attr(,"class")attr(,"package")
#> [1] "methods"
plot(params)
#> Error: unable to find an inherited method for function ‘params’ for signature ‘x = "numeric"’
f1Count(params)
#> Error: unable to find an inherited method for function ‘f1Count’ for signature ‘object = "standardGeneric"’
levelPlot(params)
#> Error: unable to find an inherited method for function ‘levelPlot’ for signature ‘object = "standardGeneric"’
getParams(params)
#> Error: unable to find an inherited method for function ‘getParams’ for signature ‘object = "standardGeneric"’
res <- plsdaClassification(dunkley2006, params)
#> Error: unable to find an inherited method for function ‘getParams’ for signature ‘object = "standardGeneric"’
getPredictions(res, fcol = "plsda")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'fData': object 'res' not found
getPredictions(res, fcol = "plsda", t = 0.9)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'fData': object 'res' not found
plot2D(res, fcol = "plsda")
#> Error: object 'res' not found
# }