MSstats_data            Testing dataset in MSstats format
OpenSWATH_data          Testing dataset from OpenSWATH
SWATH2stats-package     SWATH2stats
Spyogenes               S.pyogenes example data
Study_design            Study design table
assess_decoy_rate       assess_decoy_rate: Assess decoy rate
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         convert4MSstats: Convert table into the format
                        for MSstats
convert4aLFQ            convert4aLFQ: Convert table into the format for
                        aLFQ
convert4mapDIA          convert4mapDIA: Convert table into the format
                        for mapDIA
convert4pythonscript    convert4bashscript: Convert data into the
                        format for running a bash script
count_analytes          count_analytes: Counts analytes in different
                        injections
disaggregate            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_mscore: Filter openSWATH output table
                        according to mscore
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_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             import_data: Transforms the column names from a
                        data frame to the required format.
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           Plot functionality for FDR assessment result
                        arrays as produced by e.g. the function
                        assess_fdr_byrun()
plot.fdr_table          Plot functionality 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
sample_annotation       sample_annotation: Annotate the SWATH data with
                        the sample information
transform_MSstats_OpenSWATH
                        transform_MSstats_OpenSWATH: Transforms column
                        names to OpenSWATH column names
unifyProteinGroupLabels
                        Unify the protein group labels
write_matrix_peptides   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   write_matrix_proteins: Writes out an overview
                        matrix of summed signals per protein identifier
                        (lines) over run_id(columns).
