applyThresholdCompartment: Apply thresholds to compartments

In SubCellBarCode: SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Description

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

Usage

applyThresholdCompartment(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 compaartment

Value

c.cls.df

Examples

{

df <- loadData(SubCellBarCode::hcc827Ctrl)

c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])

set.seed(7)
c.prots <- sample(c.prots, 550)
cls <- svmClassification(c.prots, 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)
}

SubCellBarCode documentation built on Nov. 8, 2020, 5:26 p.m.