mergeCls: Merge compartment and neighborhood classification

In TanerArslan/SubCellBarCode-R-Package: SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Description

Compartment and neighborhood classifications are merged for the single output.

Usage

mergeCls(compartmentCls, neighborhoodCls)

Arguments

compartmentCls	data.frame; all predictions, including unclassified as well, and probablity vectors for each protein in compartment classification
neighborhoodCls	data.frame; all predictions, including unclassified as well, and probablity vectors for each protein in compartment classification

Value

cls.df

Examples

{

df <- loadData(SubCellBarCode::hcc827Ctrl)

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

r.markers <- markerQualityControl(c.prots, df)

cls <- svmClassification(r.markers, 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)

t.n.df <- computeThresholdNeighborhood(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)

n.cls.df <- applyThresholdNeighborhood(all.A, all.B, t.n.df)

cls.df <- mergeCls(c.cls.df, n.cls.df)
}

TanerArslan/SubCellBarCode-R-Package documentation built on May 14, 2019, 9:38 a.m.