Select alternate m_score column in JPP data and avert user

Source: R/JPP_update.R

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.

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

Peter Blattmann

Examples

{
data("OpenSWATH_data", package="SWATH2stats")
JPP_update(OpenSWATH_data, "m_score")
}
#> [1] "m_score"