Package: SWATH2stats 1.37.0

Peter Blattmann

SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.

Authors:Peter Blattmann [aut, cre] Moritz Heusel [aut] Ruedi Aebersold [aut]

SWATH2stats_1.37.0.tar.gz
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SWATH2stats.pdf |SWATH2stats.html✨
SWATH2stats/json (API)
NEWS

# Install 'SWATH2stats' in R:
install.packages('SWATH2stats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/peterblattmann/swath2stats/issues

Pkgdown:https://peterblattmann.github.io

Datasets:
  • MSstats_data - Testing dataset in MSstats format.
  • OpenSWATH_data - Testing dataset from OpenSWATH.
  • Study_design - A table containing the meta-data defining the study design of the OpenSWATH data.
  • data - Testing dataset from OpenSWATH.

On BioConductor:SWATH2stats-1.37.0(bioc 3.21)SWATH2stats-1.36.0(bioc 3.20)

proteomicsannotationexperimentaldesignpreprocessingmassspectrometryimmunooncology

6.47 score 1 stars 22 scripts 218 downloads 9 mentions 37 exports 81 dependencies

Last updated 2 months agofrom:8dd555110a. Checks:OK: 5 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winOKNov 30 2024
R-4.5-linuxOKNov 30 2024
R-4.4-winOKNov 30 2024
R-4.4-macERRORNov 30 2024
R-4.3-winOKNov 30 2024
R-4.3-macERRORNov 30 2024

Exports:add_genesymbolassess_decoy_rateassess_fdr_byrunassess_fdr_overallconvert_protein_idsconvert4aLFQconvert4mapDIAconvert4MSstatsconvert4PECAconvert4pythonscriptcount_analytesdisaggregatefilter_all_peptidesfilter_mscorefilter_mscore_conditionfilter_mscore_fdrfilter_mscore_freqobsfilter_on_max_peptidesfilter_on_min_peptidesfilter_proteotypic_peptidesimport_dataJPP_updateload_martmscore4assayfdrmscore4pepfdrmscore4protfdrplot_correlation_between_samplesplot_variationplot_variation_vs_totalreduce_OpenSWATH_outputremoveDecoyProteinssample_annotationtransform_MSstats_OpenSWATHunifyProteinGroupLabelsvalidate_columnswrite_matrix_peptideswrite_matrix_proteins

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurldata.tableDBIdbplyrdigestdplyrfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreshape2rlangRSQLiteS4VectorsscalesstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrxml2XVectorzlibbioc

SWATH2stats example script

Rendered fromSWATH2stats_example_script.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2020-10-04
Started: 2016-03-04

SWATH2stats package Vignette

Rendered fromSWATH2stats_vignette.Rnwusingutils::Sweaveon Nov 30 2024.

Last update: 2019-04-28
Started: 2015-10-06

Readme and manuals

Help Manual

Help pageTopics
Adds gene symbols to a tableadd_genesymbol
Assess decoy rate in dataassess_decoy_rate
Assess assay, peptide and protein level FDR by run (for each MS_injection separately) in OpenSWATH output tableassess_fdr_byrun
Assess overall FDR in annotated OpenSWATH/pyProphet output table in dependence of m_score cutoffassess_fdr_overall
Convert protein idsconvert_protein_ids
Convert table into the format expected by aLFQ.convert4aLFQ
Convert table into the format for mapDIAconvert4mapDIA
Get data ready for use by MSstats.convert4MSstats
Convert table into the format for ROPECAconvert4PECA
Convert data into the format for running a python script.convert4pythonscript
Counts the analytes across the different injectionscount_analytes
Transforms the SWATH data from a peptide- to a transition-level table.disaggregate
Select all proteins that are supported by peptides.filter_all_peptides
Filter OpenSWATH output table based on mscore.filter_mscore
Filter OpenSWATH output table according to mscore and conditions.filter_mscore_condition
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_fdr
Filter OpenSWATH output table according to mscore.filter_mscore_freqobs
Filter only for the highest intense peptidesfilter_on_max_peptides
Filter openSWATH output for proteins that are identified by a minimum of n independent peptides.filter_on_min_peptides
Filter for proteins that are supported by proteotypic peptides.filter_proteotypic_peptides
Transforms the column names from a data frame to the required format.import_data
Select alternate m_score column in JPP data and avert userJPP_update
Establish connection to biomaRt databaseload_mart
Find m_score cutoff to reach a desired FDR on assay level (over the entire OpenSWATH/pyProphet output table)mscore4assayfdr
Find m_score cutoff to reach a desired FDR on peptide level (over the entire OpenSWATH/pyProphet output table)mscore4pepfdr
Find m_score cutoff to reach a desired FDR on protein level (over the entire OpenSWATH/pyProphet output table)mscore4protfdr
Testing dataset in MSstats format.MSstats_data
Testing dataset from OpenSWATH.data OpenSWATH_data
Plots the correlation between injections.plot_correlation_between_samples
Plots the coefficient of variation for different replicates.plot_variation
Plots the total variation versus variation within replicatesplot_variation_vs_total
S3 plot function for FDR assessment result arraysplot.fdr_cube
S3 plot function for results of class "fdr_table" as produced by e.g. the function assess_fdr_overall()plot.fdr_table
Reduce columns of OpenSWATH datareduce_OpenSWATH_output
Removes decoy proteins from the protein group labelremoveDecoyProteins
Subfunction to remove decoysrmDecoyProt
Annotate the SWATH data with the sample informationsample_annotation
S.pyogenes example data.Spyogenes
A table containing the meta-data defining the study design of the OpenSWATH data.Study_design
Transforms column names to OpenSWATH column namestransform_MSstats_OpenSWATH
Unify the protein group labels.unifyProteinGroupLabels
Validate columns for a data.framevalidate_columns
Writes out an overview matrix of peptides mapping to a FDR quality controlled protein master list at controlled global peptide FDR quality.write_matrix_peptides
Writes out an overview matrix of summed signals per protein identifier (lines) over run_id(columns).write_matrix_proteins