candidateRelocatedProteins: Identify candidate relocated proteins

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

Description

Identify candidate condition-dependent relocated proteins by comparing neighborhood classifications with respect to protein-protein pearson correlation and minumum PSM, peptide spectrum matching, count.

Usage

candidateRelocatedProteins(sampleCls1, s1PSM, s1Quant, sampleCls2, s2PSM,
  s2Quant, annotation = FALSE, min.psm, pearson.cor)

Arguments

sampleCls1	data.frame; merged classification, combination of compartment and neighborhood classification.
s1PSM	data.frame; minimum PSM count table across ten TMT channel
s1Quant	data.frame; fractionation quantification data
sampleCls2	data.frame; merged classification, combination of compartment and neighborhood classification.
s2PSM	data.frame; minimum PSM count table across ten TMT channel
s2Quant	data.frame; fractionation quantification data
annotation	boolean; labeling the selected proteins
min.psm	numeric; minimum psm, peptide spectra matching value
pearson.cor	numeric; pearson correlation threshold

Value

candidate.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)

candidate.df <- candidateRelocatedProteins(cls.df,hcc827CtrlPSMCount,
hcc827Ctrl, hcc827GEFClass, hcc827CtrlPSMCount, hcc827GEF)

candidate.df <- candidateRelocatedProteins(cls.df, hcc827CtrlPSMCount,
hcc827Ctrl, hcc827GEFClass, hcc827CtrlPSMCount, hcc827GEF,
annotation = TRUE, min.psm = 12, pearson.cor = 0.8)

}

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