filter_mscore {SWATH2stats} | R Documentation

## filter_mscore: 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 (requant) and within a condition (condition)

### Usage

    filter_mscore(data, mscore, rm.decoy=TRUE, mscore.col = "m_score")
    filter_mscore_freqobs(data, mscore, percentage=NULL,
    rm.decoy = TRUE, mscore.col = "m_score")
    filter_mscore_condition(data, mscore, n.replica, 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.
`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 1.17.5 Index]