convert4PECA: Convert table into the format for ROPECA
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Value Note Author(s) References Examples

This functions selects the columns necessary for ROPECA.

1	convert4PECA(data)

data

A data frame containing SWATH data.

Returns a data frame in the appropriate format for ROPECA.

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

Peter Blattmann

Suomi, T. and Elo L.L. (2017). "Enhanced differential expression statistics for data-independent acquisition proteomics" Scientific Reports 7, Article number: 5869.doi:10.1038/s41598-017-05949-y

{
 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)
 data.PECA <- convert4PECA(data.filtered.decoy)
}