convert4pythonscript {SWATH2stats} | R Documentation

## convert4bashscript: Convert data into the format for running a bash 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)

[Package SWATH2stats version 1.18.0 Index]