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 1.3.4 Index]