filter_mscore_condition {SWATH2stats} | R Documentation

## Filter OpenSWATH output table according to mscore and conditions.

### Description

This function filters the SWATH data according to the m_score value, as well as to the number of occurence in the data (requant) and within a condition (condition).

### Usage

    filter_mscore_condition(
      data,
      mscore,
      n_replica,
      peptide_col = c("Peptide.Sequence", "FullPeptideName"),
      charge_col = "Charge",
      condition_col = "Condition",
      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.
`n_replica` | Number of measurements within at least one condition that have to pass the mscore threshold for this transition.
`peptide_col` | Column with peptide identifiers. Default: Peptide.Sequence or FullPeptideName
`charge_col` | Column with peptide charge. Default: Charge
`condition_col` | Column with conditions. Default: Condition
`rm.decoy` | Option to drop decoys from the data
`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

Data which has been filtered.

### 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 1.20.1 Index]