convert4mapDIA {SWATH2stats} | R Documentation

## 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 1.20.1 Index]