Transforms column names to OpenSWATH column names

Source: R/transform_MSstats_OpenSWATH.R

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, Fragmentation, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity.)

transform_MSstats_OpenSWATH(data)

Arguments

data

A data frame containing the SWATH data in the MSstats format

Value

The data frame in the appropriate format.

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.

Author

Peter Blattmann

Examples

 data("MSstats_data", package="SWATH2stats")
 transformed <- transform_MSstats_OpenSWATH(MSstats_data)
#> Additional columns present in the data: FileName
#> No column 'mscore' present in the data. This column is required for functions estimating FDR or filtering the data.