convert4mapDIA {SWATH2stats} | R Documentation

## 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.

### Note

The table must not contain any technical replica, the intensity of technical replica is averaged. This function requires the package reshape2.

### Author(s)

Peter Blattmann

### 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)

[Package SWATH2stats version 1.18.0 Index]