Convert table into the format for ROPECA

Source: R/convert4PECA.R

This functions selects the columns necessary for ROPECA.

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.

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

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)
 data.PECA <- convert4PECA(data.filtered.decoy)
}
#> Dimension difference: 931, 0