convert4MSstats: Get data ready for use by MSstats.
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Details Value Author(s) References Examples

Though SWATH2stats uses very similar format as MSstats, some coercion is required to convert the data into the format for MSstats.

convert4MSstats(
  data,
  replace_values = TRUE,
  replace_colnames = TRUE,
  replace_unimod = TRUE
)

`data`	A data frame containing SWATH data.
`replace_values`	Option to indicate if negative and 0 values should be replaced with NA.
`replace_colnames`	Option to indicate if column names should be renamed and columns reduced to the necessary columns for MSstats.
`replace_unimod`	Option to indicate if Unimod Identifier should be replaced from ":" to "_".

This functions selects the columns necessary for MSstats and renames them if necessary.

The necessary columns are selected and three columns renamed: FullPeptideName -> PeptideSequence Charge -> PrecursorCharge filename -> File

Returns a data frame in the appropriate format for MSstats.

Peter Blattmann

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.

 data("OpenSWATH_data", package="SWATH2stats")
 data("Study_design", package="SWATH2stats")
 data <- sample_annotation(OpenSWATH_data, Study_design)
 data.filtered.decoy <- filter_mscore(data, 0.01)
 raw <- disaggregate(data.filtered.decoy)
 data.mapDIA <- convert4MSstats(raw)