reduce_OpenSWATH_output {SWATH2stats} | R Documentation

## Reduce columns of OpenSWATH data

### Description

This function selects the columns from the standard OpenSWATH output to column needed for MSstats, aLFQ and mapDIA.

### Usage

    reduce_OpenSWATH_output(data, column.names=NULL)

### Arguments

`data` | A data frame containing SWATH data.
`column.names` | A vector of column names that can be selected.

### Value

Returns a data frame with the selected columns.

### Note

A basic set of columns are defined in the function and are used if no column names are indicated

### Note

The column.names can be omitted and then the following columns are selected that are needed for MSstats and mapDIA analysis: ProteinName, FullPeptideName, Sequence, Charge, aggr_Fragment_Annotation, aggr_Peak_Area, filename, m_score, decoy, Intensity, RT. This function should be ommitted if the data is analyzed afterwards with the aLFQ or imsbInfer package that needs further columns.

### Author(s)

Peter Blattmann

### Examples

    data("OpenSWATH_data", package="SWATH2stats")
    data("Study_design", package="SWATH2stats")
    data <- sample_annotation(OpenSWATH_data, Study_design)
    data.filtered <- reduce_OpenSWATH_output(data)

[Package SWATH2stats version 1.17.5 Index]