applyThresholdNeighborhood {SubCellBarCode}R Documentation

Apply thresholds to neighborhood classification

Description

Apply thresholds for all predictions at the neighborhood level to increase the true positive rate and remove poor classification.

Usage

applyThresholdNeighborhood(all.repA, all.repB, threshold.df)

Arguments

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

Value

n.cls.df

Examples

{

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)
}

[Package SubCellBarCode version 1.0.0 Index]