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

Description Usage Arguments Details Value Author(s) Examples

View source: R/convert4pythonscript.R

Description

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

Usage

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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

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 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 April 20, 2021, 12:02 p.m.