Convert data into the format for running a python script.

Source: R/convert4pythonscript.R

This functions selects the columns suggested to run a python script to change the data from peptide-level to transition-level.

convert4pythonscript(data, replace.Unimod = TRUE)

Arguments

data

A data frame containing SWATH data.

replace.Unimod

Option to indicate if Unimod Identifier should be replaced form ":"" to "_".

Value

Returns a data frame in the appropriate format to be used by a custom python script stored in the scripts folder.

Details

The necessary columns are selected and the run column is renamed to filename for the script. The intensities are taken from the column aggr_Peak_Area and therefore the Intensity column is not exported.

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)
#> Dimension difference: 931, 0
 data.pythonscript <- convert4pythonscript(data.filtered.decoy)