SWATH2stats (version 1.2.3)

convert4pythonscript: 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 "_".

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 align_origfilename for the script. The intensities are taken from the column aggr_Peak_Area and therefore the Intensity column is not exported.

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)