Man pages for SWATH2stats
Transform and Filter SWATH Data for Statistical Packages

add_genesymbolAdds gene symbols to a table
assess_decoy_rateAssess decoy rate in data
assess_fdr_byrunAssess assay, peptide and protein level FDR by run (for each...
assess_fdr_overallAssess overall FDR in annotated OpenSWATH/pyProphet output...
convert4aLFQConvert table into the format expected by aLFQ.
convert4mapDIAConvert table into the format for mapDIA
convert4MSstatsGet data ready for use by MSstats.
convert4PECAConvert table into the format for ROPECA
convert4pythonscriptConvert data into the format for running a python script.
convert_protein_idsConvert protein ids
count_analytesCounts the analytes across the different injections
disaggregateTransforms the SWATH data from a peptide- to a...
filter_all_peptidesSelect all proteins that are supported by peptides.
filter_mscoreFilter OpenSWATH output table based on mscore.
filter_mscore_conditionFilter OpenSWATH output table according to mscore and...
filter_mscore_fdrFilter annotated OpenSWATH/pyProphet output table to achieve...
filter_mscore_freqobsFilter OpenSWATH output table according to mscore.
filter_on_max_peptidesFilter only for the highest intense peptides
filter_on_min_peptidesFilter openSWATH output for proteins that are identified by a...
filter_proteotypic_peptidesFilter for proteins that are supported by proteotypic...
import_dataTransforms the column names from a data frame to the required...
JPP_updateSelect alternate m_score column in JPP data and avert user
load_martEstablish connection to biomaRt database
mscore4assayfdrFind m_score cutoff to reach a desired FDR on assay level...
mscore4pepfdrFind m_score cutoff to reach a desired FDR on peptide level...
mscore4protfdrFind m_score cutoff to reach a desired FDR on protein level...
MSstats_dataTesting dataset in MSstats format.
OpenSWATH_dataTesting dataset from OpenSWATH.
plot_correlation_between_samplesPlots the correlation between injections.
plot.fdr_cubeS3 plot function for FDR assessment result arrays
plot.fdr_tableS3 plot function for results of class "fdr_table" as produced...
plot_variationPlots the coefficient of variation for different replicates.
plot_variation_vs_totalPlots the total variation versus variation within replicates
reduce_OpenSWATH_outputReduce columns of OpenSWATH data
removeDecoyProteinsRemoves decoy proteins from the protein group label
rmDecoyProtSubfunction to remove decoys
sample_annotationAnnotate the SWATH data with the sample information
SpyogenesS.pyogenes example data.
Study_designA table containing the meta-data defining the study design of...
transform_MSstats_OpenSWATHTransforms column names to OpenSWATH column names
unifyProteinGroupLabelsUnify the protein group labels.
validate_columnsValidate columns for a data.frame
write_matrix_peptidesWrites out an overview matrix of peptides mapping to a FDR...
write_matrix_proteinsWrites out an overview matrix of summed signals per protein...
SWATH2stats documentation built on Nov. 8, 2020, 7:47 p.m.