applyThresholdNeighborhood: Apply thresholds to neighborhood classification

Description Usage Arguments Value Examples

View source: R/applyThresholdToNeighborhood.R

Description

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

Usage

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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

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{

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)
}

TanerArslan/SubCellBarCode documentation built on June 7, 2021, 9 a.m.