Classification using the naive Bayes algorithm.
Usage
nbClassification(
object,
assessRes,
scores = c("prediction", "all", "none"),
laplace,
fcol = "markers",
...
)Arguments
- object
An instance of class
"MSnSet".- assessRes
An instance of class
"GenRegRes", as generated bynbOptimisation.- scores
One of
"prediction","all"or"none"to report the score for the predicted class only, for all classes or none.- laplace
If
assessResis missing, alaplacemust be provided.- fcol
The feature meta-data containing marker definitions. Default is
markers.- ...
Additional parameters passed to
naiveBayesfrom packagee1071.
Value
An instance of class "MSnSet" with
nb and nb.scores feature variables storing the
classification results and scores respectively.
Examples
library(pRolocdata)
data(dunkley2006)
## reducing parameter search space and iterations
params <- nbOptimisation(dunkley2006, laplace = c(0, 5), times = 3)
#>
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params
#> Object of class "GenRegRes"
#> Algorithm: naiveBayes
#> Hyper-parameters:
#> laplace: 0 5
#> 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.
#> 0.9055 0.9437 0.9818 0.9624 0.9909 1.0000
#> best laplace: 0 5
plot(params)
f1Count(params)
#>
#> 5
#> 1
levelPlot(params)
getParams(params)
#> laplace
#> 5
res <- nbClassification(dunkley2006, params)
#> [1] "markers"
getPredictions(res, fcol = "naiveBayes")
#> ans
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 18 175 98 98 123
#> Plastid Ribosome TGN vacuole
#> 52 70 24 31
#> 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 ... naiveBayes.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 naiveBayes prediction (laplace=5) Fri Oct 18 17:20:30 2024
#> Added naiveBayes predictions according to global threshold = 0 Fri Oct 18 17:20:30 2024
#> MSnbase version: 1.17.12
getPredictions(res, fcol = "naiveBayes", t = 1)
#> ans
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 14 45 69 61 46
#> Plastid Ribosome TGN unknown vacuole
#> 43 35 13 336 27
#> 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 ... naiveBayes.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 naiveBayes prediction (laplace=5) Fri Oct 18 17:20:30 2024
#> Added naiveBayes predictions according to global threshold = 1 Fri Oct 18 17:20:30 2024
#> MSnbase version: 1.17.12
plot2D(res, fcol = "naiveBayes")
