filter_mscore_freqobs {SWATH2stats} | R Documentation

## Filter OpenSWATH output table according to mscore.

### Description

This function filters the SWATH data according to the m_score value, as well as to the number of occurence in the data.

### Usage

    filter_mscore_freqobs(
      data,
      mscore,
      percentage = NULL,
      rm.decoy = TRUE,
      mscore.col = "m_score"
    )

### Arguments

`data` | A data frame containing SWATH data.
`mscore` | Value that defines the mscore threshold according to which the data will be filtered.
`percentage` | Percentage in which replicas the transition has to reach the mscore threshold.
`rm.decoy` | Option to remove the decoys during filtering.
`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 a data frame with the filtered data.

### Author(s)

Peter Blattmann

### Examples

     data("OpenSWATH_data", package="SWATH2stats")
     data("Study_design", package="SWATH2stats")
     data <- sample_annotation(OpenSWATH_data, Study_design)
     data.filtered <- filter_mscore(data, 0.01)
     data.filtered <- filter_mscore_freqobs(data, 0.01, 0.8)
     data.filtered <- filter_mscore_condition(data, 0.01, 3)

[Package SWATH2stats version 1.24.0 Index]