convert4MSstats {SWATH2stats} | R Documentation

## convert4MSstats: Convert table into the format for MSstats

### Description

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

### 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

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 1.16.0 Index]