This function produces organelle-specific quantiles corresponding to the given classification scores.
orgQuants(object, fcol, scol, mcol = "markers", t, verbose = TRUE)An instance of class "MSnSet".
The name of the prediction column in the
featureData slot.
The name of the prediction score column in the
featureData slot. If missing, created by pasting
'.scores' after fcol.
The name of the column containing the training data in the
featureData slot. Default is markers.
The quantile threshold.
If TRUE, the calculated threholds are printed.
A named vector of organelle thresholds.
getPredictions to get organelle predictions based
on calculated thresholds.
library("pRolocdata")
data(dunkley2006)
res <- svmClassification(dunkley2006, fcol = "pd.markers",
sigma = 0.1, cost = 0.5)
#> [1] "pd.markers"
## 50% top predictions per class
ts <- orgQuants(res, fcol = "svm", t = .5)
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 0.3129695 0.8380783 0.7755526 0.7423607 0.7356209
#> Plastid Ribosome TGN vacuole
#> 0.7683069 0.5552199 0.5629277 0.5697818
getPredictions(res, fcol = "svm", t = ts)
#> ans
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 15 117 65 78 86
#> Plastid Ribosome TGN unknown vacuole
#> 37 40 15 211 25
#> 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 ... svm.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 svm prediction (cost=0.5 sigma=0.1) Tue Mar 12 07:14:05 2024
#> Added svm predictions according to thresholds: ER lumen = 0.31, ER membrane = 0.84, Golgi = 0.78, Mitochondrion = 0.74, PM = 0.74, Plastid = 0.77, Ribosome = 0.56, TGN = 0.56, vacuole = 0.57 Tue Mar 12 07:14:05 2024
#> MSnbase version: 1.17.12