candidateRelocatedProteins: Identify candidate relocated proteins

Description Usage Arguments Value Examples

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

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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

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SubCellBarCode documentation built on May 6, 2019, 3:59 a.m.