transform_MSstats_OpenSWATH {SWATH2stats} | R Documentation

## transform_MSstats_OpenSWATH: Transforms column names to OpenSWATH column names

### Description

This functions transforms the column names from a data frame in MSstats format to a data frame with column names used by the OpenSWATH output. The original table needs to contain at least the 10 columns defined by MSstats: ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity.)

### Usage

    transform_MSstats_OpenSWATH(data)

### Arguments

`data` | A data frame containing the SWATH data in the MSstats format

### Value

Returns the data frame in the appropriate format.

### Author(s)

Peter Blattmann

### References

Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek O. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305.

### Examples

    data("MSstats_data", package="SWATH2stats")
    transform_MSstats_OpenSWATH(MSstats_data)

[Package SWATH2stats version 1.16.0 Index]