Function reference • SWATH2stats

All functions
`JPP_update()`	Select alternate m_score column in JPP data and avert user
`MSstats_data`	Testing dataset in MSstats format.
`OpenSWATH_data` `data`	Testing dataset from OpenSWATH.
`Spyogenes`	S.pyogenes example data.
`Study_design`	A table containing the meta-data defining the study design of the OpenSWATH data.
`add_genesymbol()`	Adds gene symbols to a table
`assess_decoy_rate()`	Assess decoy rate in data
`assess_fdr_byrun()`	Assess assay, peptide and protein level FDR by run (for each MS_injection separately) in OpenSWATH output table
`assess_fdr_overall()`	Assess overall FDR in annotated OpenSWATH/pyProphet output table in dependence of m_score cutoff
`convert4MSstats()`	Get data ready for use by MSstats.
`convert4PECA()`	Convert table into the format for ROPECA
`convert4aLFQ()`	Convert table into the format expected by aLFQ.
`convert4mapDIA()`	Convert table into the format for mapDIA
`convert4pythonscript()`	Convert data into the format for running a python script.
`convert_protein_ids()`	Convert protein ids
`count_analytes()`	Counts the analytes across the different injections
`disaggregate()`	Transforms the SWATH data from a peptide- to a transition-level table.
`filter_all_peptides()`	Select all proteins that are supported by peptides.
`filter_mscore()`	Filter OpenSWATH output table based on mscore.
`filter_mscore_condition()`	Filter OpenSWATH output table according to mscore and conditions.
`filter_mscore_fdr()`	Filter annotated OpenSWATH/pyProphet output table to achieve a high FDR quality data matrix with controlled overall protein FDR and quantitative values for all peptides mapping to these high-confidence proteins (up to a desired overall peptide level FDR quality).
`filter_mscore_freqobs()`	Filter OpenSWATH output table according to mscore.
`filter_on_max_peptides()`	Filter only for the highest intense peptides
`filter_on_min_peptides()`	Filter openSWATH output for proteins that are identified by a minimum of n independent peptides.
`filter_proteotypic_peptides()`	Filter for proteins that are supported by proteotypic peptides.
`import_data()`	Transforms the column names from a data frame to the required format.
`load_mart()`	Establish connection to biomaRt database
`mscore4assayfdr()`	Find m_score cutoff to reach a desired FDR on assay level (over the entire OpenSWATH/pyProphet output table)
`mscore4pepfdr()`	Find m_score cutoff to reach a desired FDR on peptide level (over the entire OpenSWATH/pyProphet output table)
`mscore4protfdr()`	Find m_score cutoff to reach a desired FDR on protein level (over the entire OpenSWATH/pyProphet output table)
`plot(<fdr_cube>)`	S3 plot function for FDR assessment result arrays
`plot(<fdr_table>)`	S3 plot function for results of class "fdr_table" as produced by e.g. the function assess_fdr_overall()
`plot_correlation_between_samples()`	Plots the correlation between injections.
`plot_variation()`	Plots the coefficient of variation for different replicates.
`plot_variation_vs_total()`	Plots the total variation versus variation within replicates
`reduce_OpenSWATH_output()`	Reduce columns of OpenSWATH data
`removeDecoyProteins()`	Removes decoy proteins from the protein group label
`rmDecoyProt()`	Subfunction to remove decoys
`sample_annotation()`	Annotate the SWATH data with the sample information
`transform_MSstats_OpenSWATH()`	Transforms column names to OpenSWATH column names
`unifyProteinGroupLabels()`	Unify the protein group labels.
`validate_columns()`	Validate columns for a data.frame
`write_matrix_peptides()`	Writes out an overview matrix of peptides mapping to a FDR quality controlled protein master list at controlled global peptide FDR quality.
`write_matrix_proteins()`	Writes out an overview matrix of summed signals per protein identifier (lines) over run_id(columns).

Reference

All functions