# Transform and Filter SWATH Data for Statistical Packages

## Documentation for package ‘SWATH2stats’ version 1.39.0

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

## Help Pages

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
convert4aLFQ | Convert table into the format expected by aLFQ.
convert4mapDIA | Convert table into the format for mapDIA
convert4MSstats | Get data ready for use by MSstats.
convert4PECA | Convert table into the format for ROPECA
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
data | Testing dataset from OpenSWATH.
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.
JPP_update | Select alternate m_score column in JPP data and avert user
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)
MSstats_data | Testing dataset in MSstats format.
OpenSWATH_data | Testing dataset from OpenSWATH.
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
Spyogenes | S.pyogenes example data.
Study_design | A table containing the meta-data defining the study design of the OpenSWATH data.
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).