SWATH2stats (version 1.2.3)

transform_MSstats_OpenSWATH: 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.

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

MSstats_data <- data.frame(ProteinName = "Protein1", PeptideSequence = "Peptide1", 
PrecursorCharge = 1, FragmentIon = "y4",ProductCharge = 2, IsotopeLabelType = "L",
Condition = "Cond1", BioReplicate = 1, Run = 1, Intensity = 1254)
transform_MSstats_OpenSWATH(MSstats_data)