Transform and Filter SWATH Data for Statistical Packages

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Documentation for package ‘SWATH2stats’ version 1.22.0

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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).