SWATH2stats (version 1.2.3)

convert4MSstats: 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 "_".

Value

Returns a data frame in the appropriate format for MSstats.

Details

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

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)