convert4MSstats {SWATH2stats} | R Documentation

## Get data ready for use by MSstats.

### Description

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

### Usage

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

### Arguments

`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 "_".

### Details

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

### Value

Returns a data frame in the appropriate format for MSstats.

### 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("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)

[Package SWATH2stats version 1.20.1 Index]