SWATH2stats (version 1.2.3)

convert4mapDIA: convert4mapDIA: Convert table into the format for mapDIA

Description

This functions selects the columns necessary for mapDIA.

Usage

convert4mapDIA(data, RT=FALSE)

Arguments

data

A data frame containing SWATH data.

RT

Option to export the retention times.

Value

Returns a data frame in the appropriate format for mapDIA.

References

Teo, G., et al. (2015). "mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry." J Proteomics 129: 108-120.

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 <- convert4mapDIA(raw, RT=TRUE)