# Transform and Filter SWATH Data for Statistical Packages

## Documentation for package ‘SWATH2stats’ version 1.6.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

SWATH2stats-package | SWATH2stats
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
convert4aLFQ | convert4aLFQ: Convert table into the format for aLFQ
convert4mapDIA | convert4mapDIA: Convert table into the format for mapDIA
convert4MSstats | convert4MSstats: Convert table into the format for MSstats
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_condition | 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_mscore_freqobs | filter_mscore: 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 | 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)
MSstats_data | Testing dataset in MSstats format
OpenSWATH_data | Testing dataset from OpenSWATH
OpenSWATH_data_FDR | Testing dataset from OpenSWATH
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
rmDecoyProt | Removes decoy proteins from the protein group label
sample_annotation | sample_annotation: Annotate the SWATH data with the sample information
Spyogenes | S.pyogenes example data
Study_design | Study design table
SWATH2stats | SWATH2stats
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).