Description Usage Arguments Value Examples
View source: R/applyThresholdToCompartment.R
Apply thresholds for all predictions to increase the true positive rate and remove poor classification.
1 | applyThresholdCompartment(all.repA, all.repB, threshold.df)
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all.repA |
data.frame; all predictions and probablity vectors for each protein in replicate A |
all.repB |
data.frame; all predictions and probablity vectors for each protein in replicate B |
threshold.df |
data.frame; collection od precision and recall values for each compaartment |
c.cls.df
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | {
df <- loadData(SubCellBarCode::hcc827Ctrl)
c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
r.markers <- markerQualityControl(c.prots, df)
cls <- svmClassification(r.markers, df, markerProteins)
test.A <- cls[[1]]$svm.test.prob.out
test.B <- cls[[2]]$svm.test.prob.out
t.c.df <- computeThresholdCompartment(test.A, test.B)
all.A <- cls[[1]]$all.prot.pred
all.B <- cls[[2]]$all.prot.pred
c.cls.df<- applyThresholdCompartment(all.A, all.B, t.c.df)
}
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