convert4mapDIA: Convert table into the format for mapDIA

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

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)
 }

peterblattmann/SWATH2stats documentation built on July 2, 2023, 9:42 p.m.