| applyThresholdNeighborhood {SubCellBarCode} | R Documentation |
Apply thresholds for all predictions at the neighborhood level to increase the true positive rate and remove poor classification.
applyThresholdNeighborhood(all.repA, all.repB, threshold.df)
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 neighborhood |
n.cls.df
{
df <- loadData(SubCellBarCode::hcc827Ctrl)
c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
set.seed(7)
c.prots <- sample(c.prots, 600)
cls <- svmClassification(c.prots, df, markerProteins)
test.A <- cls[[1]]$svm.test.prob.out
test.B <- cls[[2]]$svm.test.prob.out
t.n.df <- computeThresholdNeighborhood(test.A, test.B)
all.A <- cls[[1]]$all.prot.pred
all.B <- cls[[2]]$all.prot.pred
n.cls.df <- applyThresholdNeighborhood(all.A, all.B, t.n.df)
}