{
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  "Package": "SWATH2stats",
  "Type": "Package",
  "Title": "Transform and Filter SWATH Data for Statistical Packages",
  "Version": "1.42.0",
  "Date": "2025-12-17",
  "Authors@R": "c(person(\"Peter\", \"Blattmann\", role = c(\"aut\", \"cre\"),\nemail=\"peter_blattmann@bluewin.ch\",\ncomment = c(ORCID = \"0000-0001-9105-6381\")),\nperson(\"Moritz\", \"Heusel\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-8506-530X\")),\nperson(\"Ruedi\", \"Aebersold\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9576-3267\")))",
  "Author": "Peter Blattmann [aut, cre] Moritz Heusel [aut] Ruedi Aebersold\n[aut]",
  "Maintainer": "Peter Blattmann <peter_blattmann@bluewin.ch>",
  "Description": "This package is intended to transform SWATH data from the\nOpenSWATH software into a format readable by other statistics\npackages while performing filtering, annotation and FDR\nestimation.",
  "License": "GPL-3",
  "biocViews": "Proteomics, Annotation, ExperimentalDesign, Preprocessing,\nMassSpectrometry, ImmunoOncology",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:01 UTC",
  "RemoteUrl": "https://github.com/bioc/SWATH2stats",
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    "experimentaldesign",
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    "assess_decoy_rate",
    "assess_fdr_byrun",
    "assess_fdr_overall",
    "convert_protein_ids",
    "convert4aLFQ",
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    "filter_mscore",
    "filter_mscore_condition",
    "filter_mscore_fdr",
    "filter_mscore_freqobs",
    "filter_on_max_peptides",
    "filter_on_min_peptides",
    "filter_proteotypic_peptides",
    "import_data",
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    "load_mart",
    "mscore4assayfdr",
    "mscore4pepfdr",
    "mscore4protfdr",
    "plot_correlation_between_samples",
    "plot_variation",
    "plot_variation_vs_total",
    "reduce_OpenSWATH_output",
    "removeDecoyProteins",
    "sample_annotation",
    "transform_MSstats_OpenSWATH",
    "unifyProteinGroupLabels",
    "validate_columns",
    "write_matrix_peptides",
    "write_matrix_proteins"
  ],
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      "name": "data",
      "title": "Testing dataset from OpenSWATH.",
      "object": "Spyogenes",
      "file": "Spyogenes.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ProteinName",
        "FullPeptideName",
        "Charge",
        "aggr_Fragment_Annotation",
        "aggr_Peak_Area",
        "transition_group_id",
        "decoy",
        "m_score",
        "RT",
        "align_origfilename",
        "Intensity",
        "Sequence",
        "delta_rt"
      ],
      "rows": 38272,
      "table": true,
      "tojson": true
    },
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      "name": "MSstats_data",
      "title": "Testing dataset in MSstats format.",
      "object": "MSstats_data",
      "file": "MSstats_data.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ProteinName",
        "PeptideSequence",
        "PrecursorCharge",
        "FragmentIon",
        "ProductCharge",
        "IsotopeLabelType",
        "Condition",
        "BioReplicate",
        "Run",
        "FileName",
        "Intensity"
      ],
      "rows": 6,
      "table": true,
      "tojson": true
    },
    {
      "name": "OpenSWATH_data",
      "title": "Testing dataset from OpenSWATH.",
      "object": "OpenSWATH_data",
      "file": "OpenSWATH_data.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "transition_group_id",
        "peptide_group_label",
        "run_id",
        "filename",
        "RT",
        "id",
        "Sequence",
        "FullPeptideName",
        "Charge",
        "m.z",
        "Intensity",
        "ProteinName",
        "decoy",
        "assay_rt",
        "delta_rt",
        "leftWidth",
        "main_var_xx_swath_prelim_score",
        "norm_RT",
        "nr_peaks",
        "peak_apices_sum",
        "potentialOutlier",
        "rightWidth",
        "rt_score",
        "sn_ratio",
        "total_xic",
        "var_bseries_score",
        "dotprod_score",
        "var_intensity_score",
        "var_isotope_correlation_score",
        "var_isotope_overlap_score",
        "var_library_corr",
        "library_dotprod",
        "library_manhattan",
        "var_library_rmsd",
        "library_rootmeansquare",
        "library_sangle",
        "var_log_sn_score",
        "manhatt_score",
        "var_massdev_score",
        "var_massdev_score_weighted",
        "var_norm_rt_score",
        "var_xcorr_coelution",
        "var_xcorr_coelution_weighted",
        "var_xcorr_shape",
        "var_xcorr_shape_weighted",
        "var_yseries_score",
        "elution_model_fit_score",
        "xx_lda_prelim_score",
        "xx_swath_prelim_score",
        "aggr_Peak_Area",
        "aggr_Peak_Apex",
        "aggr_Fragment_Annotation",
        "d_score",
        "m_score",
        "peak_group_rank",
        "align_runid",
        "align_origfilename",
        "align_clusterid"
      ],
      "rows": 2369,
      "table": true,
      "tojson": true
    },
    {
      "name": "Study_design",
      "title": "A table containing the meta-data defining the study design of the OpenSWATH data.",
      "object": "Study_design",
      "file": "Study_design.txt.gz",
      "class": [
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      ],
      "fields": [
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        "Condition",
        "BioReplicate",
        "Run"
      ],
      "rows": 6,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_genesymbol",
      "title": "Adds gene symbols to a table",
      "topics": [
        "add_genesymbol"
      ]
    },
    {
      "page": "assess_decoy_rate",
      "title": "Assess decoy rate in data",
      "topics": [
        "assess_decoy_rate"
      ]
    },
    {
      "page": "assess_fdr_byrun",
      "title": "Assess assay, peptide and protein level FDR by run (for each MS_injection separately) in OpenSWATH output table",
      "topics": [
        "assess_fdr_byrun"
      ]
    },
    {
      "page": "assess_fdr_overall",
      "title": "Assess overall FDR in annotated OpenSWATH/pyProphet output table in dependence of m_score cutoff",
      "topics": [
        "assess_fdr_overall"
      ]
    },
    {
      "page": "convert_protein_ids",
      "title": "Convert protein ids",
      "topics": [
        "convert_protein_ids"
      ]
    },
    {
      "page": "convert4aLFQ",
      "title": "Convert table into the format expected by aLFQ.",
      "topics": [
        "convert4aLFQ"
      ]
    },
    {
      "page": "convert4mapDIA",
      "title": "Convert table into the format for mapDIA",
      "topics": [
        "convert4mapDIA"
      ]
    },
    {
      "page": "convert4MSstats",
      "title": "Get data ready for use by MSstats.",
      "topics": [
        "convert4MSstats"
      ]
    },
    {
      "page": "convert4PECA",
      "title": "Convert table into the format for ROPECA",
      "topics": [
        "convert4PECA"
      ]
    },
    {
      "page": "convert4pythonscript",
      "title": "Convert data into the format for running a python script.",
      "topics": [
        "convert4pythonscript"
      ]
    },
    {
      "page": "count_analytes",
      "title": "Counts the analytes across the different injections",
      "topics": [
        "count_analytes"
      ]
    },
    {
      "page": "disaggregate",
      "title": "Transforms the SWATH data from a peptide- to a transition-level table.",
      "topics": [
        "disaggregate"
      ]
    },
    {
      "page": "filter_all_peptides",
      "title": "Select all proteins that are supported by peptides.",
      "topics": [
        "filter_all_peptides"
      ]
    },
    {
      "page": "filter_mscore",
      "title": "Filter OpenSWATH output table based on mscore.",
      "topics": [
        "filter_mscore"
      ]
    },
    {
      "page": "filter_mscore_condition",
      "title": "Filter OpenSWATH output table according to mscore and conditions.",
      "topics": [
        "filter_mscore_condition"
      ]
    },
    {
      "page": "filter_mscore_fdr",
      "title": "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).",
      "topics": [
        "filter_mscore_fdr"
      ]
    },
    {
      "page": "filter_mscore_freqobs",
      "title": "Filter OpenSWATH output table according to mscore.",
      "topics": [
        "filter_mscore_freqobs"
      ]
    },
    {
      "page": "filter_on_max_peptides",
      "title": "Filter only for the highest intense peptides",
      "topics": [
        "filter_on_max_peptides"
      ]
    },
    {
      "page": "filter_on_min_peptides",
      "title": "Filter openSWATH output for proteins that are identified by a minimum of n independent peptides.",
      "topics": [
        "filter_on_min_peptides"
      ]
    },
    {
      "page": "filter_proteotypic_peptides",
      "title": "Filter for proteins that are supported by proteotypic peptides.",
      "topics": [
        "filter_proteotypic_peptides"
      ]
    },
    {
      "page": "import_data",
      "title": "Transforms the column names from a data frame to the required format.",
      "topics": [
        "import_data"
      ]
    },
    {
      "page": "JPP_update",
      "title": "Select alternate m_score column in JPP data and avert user",
      "topics": [
        "JPP_update"
      ]
    },
    {
      "page": "load_mart",
      "title": "Establish connection to biomaRt database",
      "topics": [
        "load_mart"
      ]
    },
    {
      "page": "mscore4assayfdr",
      "title": "Find m_score cutoff to reach a desired FDR on assay level (over the entire OpenSWATH/pyProphet output table)",
      "topics": [
        "mscore4assayfdr"
      ]
    },
    {
      "page": "mscore4pepfdr",
      "title": "Find m_score cutoff to reach a desired FDR on peptide level (over the entire OpenSWATH/pyProphet output table)",
      "topics": [
        "mscore4pepfdr"
      ]
    },
    {
      "page": "mscore4protfdr",
      "title": "Find m_score cutoff to reach a desired FDR on protein level (over the entire OpenSWATH/pyProphet output table)",
      "topics": [
        "mscore4protfdr"
      ]
    },
    {
      "page": "MSstats_data",
      "title": "Testing dataset in MSstats format.",
      "topics": [
        "MSstats_data"
      ]
    },
    {
      "page": "OpenSWATH_data",
      "title": "Testing dataset from OpenSWATH.",
      "topics": [
        "data",
        "OpenSWATH_data"
      ]
    },
    {
      "page": "plot_correlation_between_samples",
      "title": "Plots the correlation between injections.",
      "topics": [
        "plot_correlation_between_samples"
      ]
    },
    {
      "page": "plot_variation",
      "title": "Plots the coefficient of variation for different replicates.",
      "topics": [
        "plot_variation"
      ]
    },
    {
      "page": "plot_variation_vs_total",
      "title": "Plots the total variation versus variation within replicates",
      "topics": [
        "plot_variation_vs_total"
      ]
    },
    {
      "page": "plot.fdr_cube",
      "title": "S3 plot function for FDR assessment result arrays",
      "topics": [
        "plot.fdr_cube"
      ]
    },
    {
      "page": "plot.fdr_table",
      "title": "S3 plot function for results of class \"fdr_table\" as produced by e.g. the function assess_fdr_overall()",
      "topics": [
        "plot.fdr_table"
      ]
    },
    {
      "page": "reduce_OpenSWATH_output",
      "title": "Reduce columns of OpenSWATH data",
      "topics": [
        "reduce_OpenSWATH_output"
      ]
    },
    {
      "page": "removeDecoyProteins",
      "title": "Removes decoy proteins from the protein group label",
      "topics": [
        "removeDecoyProteins"
      ]
    },
    {
      "page": "rmDecoyProt",
      "title": "Subfunction to remove decoys",
      "topics": [
        "rmDecoyProt"
      ]
    },
    {
      "page": "sample_annotation",
      "title": "Annotate the SWATH data with the sample information",
      "topics": [
        "sample_annotation"
      ]
    },
    {
      "page": "Spyogenes",
      "title": "S.pyogenes example data.",
      "topics": [
        "Spyogenes"
      ]
    },
    {
      "page": "Study_design",
      "title": "A table containing the meta-data defining the study design of the OpenSWATH data.",
      "topics": [
        "Study_design"
      ]
    },
    {
      "page": "transform_MSstats_OpenSWATH",
      "title": "Transforms column names to OpenSWATH column names",
      "topics": [
        "transform_MSstats_OpenSWATH"
      ]
    },
    {
      "page": "unifyProteinGroupLabels",
      "title": "Unify the protein group labels.",
      "topics": [
        "unifyProteinGroupLabels"
      ]
    },
    {
      "page": "validate_columns",
      "title": "Validate columns for a data.frame",
      "topics": [
        "validate_columns"
      ]
    },
    {
      "page": "write_matrix_peptides",
      "title": "Writes out an overview matrix of peptides mapping to a FDR quality controlled protein master list at controlled global peptide FDR quality.",
      "topics": [
        "write_matrix_peptides"
      ]
    },
    {
      "page": "write_matrix_proteins",
      "title": "Writes out an overview matrix of summed signals per protein identifier (lines) over run_id(columns).",
      "topics": [
        "write_matrix_proteins"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SWATH2stats/raw/RELEASE_3_23/README.md",
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