This function produces organelle-specific quantiles corresponding to the given classification scores.
Arguments
- object
An instance of class
"MSnSet"
.- fcol
The name of the prediction column in the
featureData
slot.- scol
The name of the prediction score column in the
featureData
slot. If missing, created by pasting '.scores' afterfcol
.- mcol
The name of the column containing the training data in the
featureData
slot. Default ismarkers
.- t
The quantile threshold.
- verbose
If
TRUE
, the calculated threholds are printed.
See also
getPredictions
to get organelle predictions based
on calculated thresholds.
Examples
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
#> 0.3317333 0.8408778 0.7704946 0.7454902 0.7358157
#> Plastid Ribosome TGN vacuole
#> 0.7733089 0.5635351 0.5184457 0.5735586
getPredictions(res, fcol = "svm", t = ts)
#> ans
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 15 117 65 78 85
#> Plastid Ribosome TGN unknown vacuole
#> 36 39 15 213 26
#> 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) Fri Oct 18 17:20:35 2024
#> Added svm predictions according to thresholds: ER lumen = 0.33, ER membrane = 0.84, Golgi = 0.77, Mitochondrion = 0.75, PM = 0.74, Plastid = 0.77, Ribosome = 0.56, TGN = 0.52, vacuole = 0.57 Fri Oct 18 17:20:35 2024
#> MSnbase version: 1.17.12