convert4pythonscript: Convert data into the format for running a python script.

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

Convert data into the format for running a python script.

Description

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

Usage

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 "_".

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.

Value

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

Author(s)

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.pythonscript <- convert4pythonscript(data.filtered.decoy)

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