Classification using the artificial neural network algorithm.
Usage
nnetClassification(
object,
assessRes,
scores = c("prediction", "all", "none"),
decay,
size,
fcol = "markers",
...
)Arguments
- object
An instance of class
"MSnSet".- assessRes
An instance of class
"GenRegRes", as generated bynnetOptimisation.- scores
One of
"prediction","all"or"none"to report the score for the predicted class only, for all classes or none.- decay
If
assessResis missing, adecaymust be provided.- size
If
assessResis missing, asizemust be provided.- fcol
The feature meta-data containing marker definitions. Default is
markers.- ...
Additional parameters passed to
nnetfrom packagennet.
Value
An instance of class "MSnSet" with
nnet and nnet.scores feature variables storing
the classification results and scores respectively.
Examples
library(pRolocdata)
data(dunkley2006)
## reducing parameter search space and iterations
params <- nnetOptimisation(dunkley2006, decay = 10^(c(-1, -5)), size = c(5, 10), times = 3)
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params
#> Object of class "GenRegRes"
#> Algorithm: nnet
#> Hyper-parameters:
#> decay: 0.1 1e-05
#> size: 5 10
#> Design:
#> Replication: 3 x 5-fold X-validation
#> Partitioning: 0.2/0.8 (test/train)
#> Results
#> macro F1:
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> 0.9315 0.9497 0.9680 0.9562 0.9686 0.9692
#> best decay: 1e-05
#> best size: 10
plot(params)
f1Count(params)
#> 10
#> 1e-05 1
levelPlot(params)
getParams(params)
#> decay size
#> 1e-05 1e+01
res <- nnetClassification(dunkley2006, params)
#> [1] "markers"
#> # weights: 269
#> initial value 697.695219
#> iter 10 value 330.822942
#> iter 20 value 62.982498
#> iter 30 value 6.342970
#> iter 40 value 2.218304
#> iter 50 value 1.029739
#> iter 60 value 0.812753
#> iter 70 value 0.663665
#> iter 80 value 0.487229
#> iter 90 value 0.413383
#> iter 100 value 0.372197
#> final value 0.372197
#> stopped after 100 iterations
getPredictions(res, fcol = "nnet")
#> ans
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 17 173 94 104 134
#> Plastid Ribosome TGN vacuole
#> 51 61 22 33
#> MSnSet (storageMode: lockedEnvironment)
#> assayData: 689 features, 16 samples
#> element names: exprs
#> protocolData: none
#> phenoData
#> sampleNames: M1F1A M1F4A ... M2F11B (16 total)
#> varLabels: membrane.prep fraction replicate
#> varMetadata: labelDescription
#> featureData
#> featureNames: AT1G09210 AT1G21750 ... AT4G39080 (689 total)
#> fvarLabels: assigned evidence ... nnet.pred (11 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> pubMedIds: 16618929
#> Annotation:
#> - - - Processing information - - -
#> Loaded on Thu Jul 16 22:53:08 2015.
#> Normalised to sum of intensities.
#> Added markers from 'mrk' marker vector. Thu Jul 16 22:53:08 2015
#> Performed nnet prediction (decay=1e-05 size=10) Fri Oct 18 17:20:34 2024
#> Added nnet predictions according to global threshold = 0 Fri Oct 18 17:20:34 2024
#> MSnbase version: 1.17.12
getPredictions(res, fcol = "nnet", t = 0.75)
#> ans
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 17 170 92 102 128
#> Plastid Ribosome TGN unknown vacuole
#> 51 58 20 19 32
#> MSnSet (storageMode: lockedEnvironment)
#> assayData: 689 features, 16 samples
#> element names: exprs
#> protocolData: none
#> phenoData
#> sampleNames: M1F1A M1F4A ... M2F11B (16 total)
#> varLabels: membrane.prep fraction replicate
#> varMetadata: labelDescription
#> featureData
#> featureNames: AT1G09210 AT1G21750 ... AT4G39080 (689 total)
#> fvarLabels: assigned evidence ... nnet.pred (11 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> pubMedIds: 16618929
#> Annotation:
#> - - - Processing information - - -
#> Loaded on Thu Jul 16 22:53:08 2015.
#> Normalised to sum of intensities.
#> Added markers from 'mrk' marker vector. Thu Jul 16 22:53:08 2015
#> Performed nnet prediction (decay=1e-05 size=10) Fri Oct 18 17:20:34 2024
#> Added nnet predictions according to global threshold = 0.75 Fri Oct 18 17:20:34 2024
#> MSnbase version: 1.17.12
plot2D(res, fcol = "nnet")
