candidateRelocatedProteins {SubCellBarCode}R Documentation

Identify candidate relocated proteins

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 = 2,
  pearson.cor = 0.8
)

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

{

candidate.df <- candidateRelocatedProteins(hcc827GEFClass, hcc827GefPSMCount,
hcc827GEF, hcc827GEFClass, hcc827GefPSMCount, hcc827GEF,
annotation = FALSE)


}

[Package SubCellBarCode version 1.10.0 Index]