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]