convert4PECA {SWATH2stats} | R Documentation

## convert4PECA: Convert table into the format for ROPECA

### Description

This functions selects the columns necessary for ROPECA.

### Usage

    convert4PECA(data)

### Arguments

`data` | A data frame containing SWATH data.

### Value

Returns a data frame in the appropriate format for ROPECA.

### 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

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

### Examples

    library(SWATH2stats)
    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)

[Package SWATH2stats version 1.10.2 Index]