JPP_update {SWATH2stats} | R Documentation

## Select alternate m_score column in JPP data and avert user

### Description

The output from JPP (Rosenberger, Bludau et al. 2017) has not anymore the m_score column but an ProteinName_m_score and transition_group_id_m_score. To make the users aware this function tests if the m_score column still exists and selects as default the transition_group_id_m_score column.

### Usage

    JPP_update(data, mscore_col)

### Arguments

`data` | Data table that is produced by the OpenSWATH/pyProphet workflow
`mscore_col` | Defines the column from which to retrieve the m_score. If you use JPP (Rosenberger, Bludau et al. 2017) this can be used to select between Protein and transition_group m_score.

### Value

Returns the mscore_col that might have been changed to transition_group_id_m_score and gives a message to the user.

### Author(s)

Peter Blattmann

### Examples

    {
    data("OpenSWATH_data", package="SWATH2stats")
    JPP_update(OpenSWATH_data, "m_score")
    }

[Package SWATH2stats version 1.20.1 Index]