Convert table into the format for mapDIA — convert4mapDIA • SWATH2stats

This functions selects the columns necessary for mapDIA.

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.

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.

Author

Peter Blattmann

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)
 }
#> Dimension difference: 931, 0
#> The library contains 6 transitions per precursor.
#>                   
#> The data table was transformed into a table containing one row per transition.