JPP_update: Select alternate m_score column in JPP data and avert user

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

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")
}

peterblattmann/SWATH2stats documentation built on July 2, 2023, 9:42 p.m.