{
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  "Package": "proteinDiscover",
  "Type": "Package",
  "Title": "ProteinDiscover",
  "Version": "0.11.0",
  "Author": "Ben Bruyneel <benbruyneel@gmail.com>",
  "Maintainer": "Ben Bruyneel <benbruyneel@gmail.com>",
  "Description": "Provides an interface to the data contained in Proteome\nDiscoverer (Thermo Scientific) results.",
  "License": "GPL (>= 3)",
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  "Date/Publication": "2024-03-14 20:22:22 UTC",
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  "_topics": [
    "mass-spectrometry",
    "proteomics",
    "proteomics-data-analysis"
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  "_exports": [
    "allNodesTable",
    "analysisDefinition",
    "blobLength",
    "calcAllIFIs",
    "calcData",
    "calcIFIs",
    "columnSpecials",
    "createDiagrammeRString",
    "dbClose",
    "dbGetAnnotatedProteins",
    "dbGetAnnotationGroups",
    "dbGetAnnotationGroupsFiltered",
    "dbGetConsensusIDs",
    "dbGetConsensusTable",
    "dbGetMassSpectrumItems",
    "dbGetModificationPeptideIDs",
    "dbGetModificationsSitesIDs",
    "dbGetModificationsTable",
    "dbGetMSnSpectrumInfo",
    "dbGetPeptideIDs",
    "dbGetPeptideTable",
    "dbGetProteinAnnotationGroupIDs",
    "dbGetProteinFiltered",
    "dbGetProteinGroupIDs",
    "dbGetProteinGroups",
    "dbGetProteinIDs",
    "dbGetProteins",
    "dbGetProteinTable",
    "dbGetProteinUniqueSequenceIDs",
    "dbGetPsmIDs",
    "dbGetPsmTable",
    "dbGetQuanSpectrumIDs",
    "dbGetQuanSpectrumInfoTable",
    "dbGetTable",
    "dbOpen",
    "determineBlobTypes",
    "df_replace",
    "dfTransformRaws",
    "getAcquistionDate",
    "getAcquistionDateTime",
    "getBlobs",
    "getPeptideInfo",
    "getPeptideInfoRaw",
    "getProteinInfo",
    "getProteinInfoRaw",
    "isMasterProtein",
    "knockOutProteins",
    "MSfileInfo",
    "na.date",
    "nodes",
    "nodeTable",
    "pQuanInfo",
    "proteinIDTypes",
    "psmAmbiguity",
    "quanInfo",
    "quanInfoDetails",
    "replacementStrings",
    "SearchInfo",
    "spectrum.centroid",
    "spectrum.header",
    "spectrum.precursor.additionalInfo",
    "spectrum.precursor.centroid",
    "spectrum.precursor.header",
    "spectrum.precursor.info",
    "spectrum.precursor.profile",
    "spectrum.precursor.scanEvent",
    "spectrum.profile",
    "spectrum.scanEvent",
    "studyDefinitionExtensions",
    "studyDefinitionExtensionSettings",
    "studyDefinitionFactors",
    "studyDefinitionFileSets",
    "studyDefinitionQuanMethods",
    "studyDefinitionSamples",
    "system.date",
    "tableNames",
    "thermo.date",
    "tmt10Channels",
    "tmt11Channels",
    "totalSearchTime",
    "transformSpectrumRaw",
    "workflowInfo"
  ],
  "_help": [
    {
      "page": "allNodesTable",
      "title": "Helper function that takes the result from the 'nodes' function, which is a named list of parameter tables (from processing or consensus workflow), and puts it all in a single table with the names of the nodes as an extra column",
      "topics": [
        "allNodesTable"
      ]
    },
    {
      "page": "analysisDefinition",
      "title": "function that gets the first element of the AnalysisDefinitionXML column from the AnalysisDefinition table in a .pdResult file",
      "topics": [
        "analysisDefinition"
      ]
    },
    {
      "page": "blobLength",
      "title": "attempts to determine the length (in bytes) of the individual elements of a blob-type column of a data.frame. It should (!) return an integer value of course (as all elements are supposed to have the same length). Also: if all elements of the column are NA, the the result will be NaN",
      "topics": [
        "blobLength"
      ]
    },
    {
      "page": "calcAllIFIs",
      "title": "Wrapper function that uses 'tmt11Channels' to calculate the IFI's for a set of (knock out) protein channels",
      "topics": [
        "calcAllIFIs"
      ]
    },
    {
      "page": "calcData",
      "title": "helper function to calculate a row-wise function (like mean, median etc) across a data.frame",
      "topics": [
        "calcData"
      ]
    },
    {
      "page": "calcIFIs",
      "title": "function to calculate the IFI (interference free index) of a protein entry in the protein table of a pdResult files. Note this can only be calculated on the knockout proteins in the TKO control sample: see 'tmt10Channels' or 'tmt11Channels' for the eligible proteins",
      "topics": [
        "calcIFIs"
      ]
    },
    {
      "page": "columnSpecials",
      "title": "Specials are not numeric or integer, but have chunks of a certain size All encountered in Proteome Discoverer are actually booleans with a value 0 (FALSE), 1 (TRUE) or NA",
      "topics": [
        "columnSpecials"
      ]
    },
    {
      "page": "createDiagrammeRString",
      "title": "function to create a DiagrammeR string that can be used by DiagrammeR::grViz() to plot a visual representation of the workflow",
      "topics": [
        "createDiagrammeRString"
      ]
    },
    {
      "page": "dbClose",
      "title": "Wrapper around pool::pooClose(): closes an open database (normally opened earlier via eg db_open())",
      "topics": [
        "dbClose"
      ]
    },
    {
      "page": "dbGetAnnotatedProteins",
      "title": "Function to get the UniqueSequenceID's for proteins which are in an protein annotation group. Essentially does the reverse of 'dbGetProteinAnnotationGroupIDs'. The output of this function can serve as the input for 'dbGetProteins'",
      "topics": [
        "dbGetAnnotatedProteins"
      ]
    },
    {
      "page": "dbGetAnnotationGroups",
      "title": "Function to get the info for (protein) annotation groups. Takes eg 'dbGetProteinAnnotationGroupIDs' as input",
      "topics": [
        "dbGetAnnotationGroups"
      ]
    },
    {
      "page": "dbGetAnnotationGroupsFiltered",
      "title": "Get Group Annotation information from the table: AnnotationProteinGroups.  This can be done via the GroupAnnotationAccession or via the description of an annotation. When using the Description it's possible to use the SQL 'like'",
      "topics": [
        "dbGetAnnotationGroupsFiltered"
      ]
    },
    {
      "page": "dbGetConsensusIDs",
      "title": "get the ConsensusID's from (a set of) PeptideGroupIDs",
      "topics": [
        "dbGetConsensusIDs"
      ]
    },
    {
      "page": "dbGetConsensusTable",
      "title": "get the Consensus Features table belonging to the ConsensusIDs",
      "topics": [
        "dbGetConsensusTable"
      ]
    },
    {
      "page": "dbGetMassSpectrumItems",
      "title": "get the MassSpectrumItems info from (a set of) PeptideID's",
      "topics": [
        "dbGetMassSpectrumItems"
      ]
    },
    {
      "page": "dbGetModificationPeptideIDs",
      "title": "Function to get the peptideID's 'belonging' to a modification site",
      "topics": [
        "dbGetModificationPeptideIDs"
      ]
    },
    {
      "page": "dbGetModificationsSitesIDs",
      "title": "function to get the modificationSite ID's from (a set of) proteinUniqueID's",
      "topics": [
        "dbGetModificationsSitesIDs"
      ]
    },
    {
      "page": "dbGetModificationsTable",
      "title": "function to get data from the ModificationSides table using the modificiationSiteId's",
      "topics": [
        "dbGetModificationsTable"
      ]
    },
    {
      "page": "dbGetMSnSpectrumInfo",
      "title": "get the MSnSpectrumInfo from (a set of) PeptideID's",
      "topics": [
        "dbGetMSnSpectrumInfo"
      ]
    },
    {
      "page": "dbGetPeptideIDs",
      "title": "get the peptideID's from (a set of) proteinGroupIDs",
      "topics": [
        "dbGetPeptideIDs"
      ]
    },
    {
      "page": "dbGetPeptideTable",
      "title": "get the paptide table belonging defined by PeptideIDs ot proteinGroupIDs",
      "topics": [
        "dbGetPeptideTable"
      ]
    },
    {
      "page": "dbGetProteinAnnotationGroupIDs",
      "title": "Function to get the functional group annotation group ID's for proteins.  This function does essentially the reverse of 'dbGetAnnotatedProteins'. The output of this function can serve as the input for 'dbGetAnnotationGroups'",
      "topics": [
        "dbGetProteinAnnotationGroupIDs"
      ]
    },
    {
      "page": "dbGetProteinFiltered",
      "title": "A bit more advanced version of 'dbGetProteinTable' which allows for filtering (via SQL). Note that filtering raw columns (BLOB's) will not work properly",
      "topics": [
        "dbGetProteinFiltered"
      ]
    },
    {
      "page": "dbGetProteinGroupIDs",
      "title": "Retrieve the ProteinGroupID's of proteins via their UniqueSequenceID's",
      "topics": [
        "dbGetProteinGroupIDs"
      ]
    },
    {
      "page": "dbGetProteinGroups",
      "title": "Gets the ProteinGroup information from the TargetProteinGroups table",
      "topics": [
        "dbGetProteinGroups"
      ]
    },
    {
      "page": "dbGetProteinIDs",
      "title": "Function to get proteinUniqueID's from a (set of) protein groupID's (eg from a proteinGroup tables, or dbGetProteinGroupIDs). This allows for getting all proteins (also non-master proteins) which together make up a protein group. Normally only the master protein is shown in a protein table",
      "topics": [
        "dbGetProteinIDs"
      ]
    },
    {
      "page": "dbGetProteins",
      "title": "Function to get protein information from the TargetProteins table on the basis of their UniqueSequenceID",
      "topics": [
        "dbGetProteins"
      ]
    },
    {
      "page": "dbGetProteinTable",
      "title": "get the protein table from a .pdResult file (essentially a wrapper around db_getTable())",
      "topics": [
        "dbGetProteinTable"
      ]
    },
    {
      "page": "dbGetProteinUniqueSequenceIDs",
      "title": "Function to retrieve the UniqueSequenceID's based on the accession field of the proteinTable. Essentially a wrapper for 'dbGetProteinFiltered'",
      "topics": [
        "dbGetProteinUniqueSequenceIDs"
      ]
    },
    {
      "page": "dbGetPsmIDs",
      "title": "get the PsmID's from (a set of) PeptideGroupIDs",
      "topics": [
        "dbGetPsmIDs"
      ]
    },
    {
      "page": "dbGetPsmTable",
      "title": "get the PSM table belonging to the PsmIDs",
      "topics": [
        "dbGetPsmTable"
      ]
    },
    {
      "page": "dbGetQuanSpectrumIDs",
      "title": "get the SpectrumID's from (a set of) PeptideIDs",
      "topics": [
        "dbGetQuanSpectrumIDs"
      ]
    },
    {
      "page": "dbGetQuanSpectrumInfoTable",
      "title": "get the QuanSpectrumInfo table belonging to the SpectrumID's",
      "topics": [
        "dbGetQuanSpectrumInfoTable"
      ]
    },
    {
      "page": "dbGetTable",
      "title": "get a table from a .pdResult file",
      "topics": [
        "dbGetTable"
      ]
    },
    {
      "page": "dbOpen",
      "title": "Wrapper around pool::dbPool(): opens a database",
      "topics": [
        "dbOpen"
      ]
    },
    {
      "page": "determineBlobTypes",
      "title": "function that attempts to assign types and sizes to the blob type columns in a table. The result from this function can be used in the dfTransformRaws function",
      "topics": [
        "determineBlobTypes"
      ]
    },
    {
      "page": "df_replace",
      "title": "function that replaces (parts of) strings in a data.frame according to a provided table of replacements",
      "topics": [
        "df_replace"
      ]
    },
    {
      "page": "dfTransformRaws",
      "title": "df_transform_raws(): converts raw columns in a data.frame to the correct data types",
      "topics": [
        "dfTransformRaws"
      ]
    },
    {
      "page": "getAcquistionDate",
      "title": "function to retrieve the acquisition date of the files used to generate the pdResult file",
      "topics": [
        "getAcquistionDate"
      ]
    },
    {
      "page": "getAcquistionDateTime",
      "title": "function to retrieve the acquisition date & time of the files used to generate the pdResult file",
      "topics": [
        "getAcquistionDateTime"
      ]
    },
    {
      "page": "getBlobs",
      "title": "detemines which columns in a table are of the blob (raw) type",
      "topics": [
        "getBlobs"
      ]
    },
    {
      "page": "getPeptideInfo",
      "title": "get peptide information from the peptide table from a pdResult file based on the provided proteinAccession (uniprot) codes. Raw columns are \"translated\"",
      "topics": [
        "getPeptideInfo"
      ]
    },
    {
      "page": "getPeptideInfoRaw",
      "title": "get peptide information from the peptide table from a pdResult file based on the provided proteinAccession (uniprot) codes. Raw columns are not \"translated\"",
      "topics": [
        "getPeptideInfoRaw"
      ]
    },
    {
      "page": "getProteinInfo",
      "title": "get protein info (with translation of columns) from a list of protein Accessions (uniprot code). Essentially this is a wrapper function for 'getProteinInfoRaw'",
      "topics": [
        "getProteinInfo"
      ]
    },
    {
      "page": "getProteinInfoRaw",
      "title": "get protein info (without translation of columns) from a list of protein Accessions (uniprot code). Essentially this is a wrapper function for 'dbGetTable'",
      "topics": [
        "getProteinInfoRaw"
      ]
    },
    {
      "page": "isMasterProtein",
      "title": "function for 'translation' of the isMasterProtein values (0..4) in the proteinTable to words (like in Proteome Discoverer).",
      "topics": [
        "isMasterProtein"
      ]
    },
    {
      "page": "knockOutProteins",
      "title": "helper function to generate the a data.frame of proteins info for other functions",
      "topics": [
        "knockOutProteins"
      ]
    },
    {
      "page": "MSfileInfo",
      "title": "get the table with info on the files used in the search from the database",
      "topics": [
        "MSfileInfo"
      ]
    },
    {
      "page": "na.date",
      "title": "fake converter for times when no conversion is wanted/needed",
      "topics": [
        "na.date"
      ]
    },
    {
      "page": "nodes",
      "title": "function that takes a (xmlToList type) workflow and returns a list of nodes",
      "topics": [
        "nodes"
      ]
    },
    {
      "page": "nodeTable",
      "title": "function to display an overview table of the processing/consensus workflows in the nodeInfo coming out of the workflowInfo function",
      "topics": [
        "nodeTable"
      ]
    },
    {
      "page": "pQuanInfo",
      "title": "function for translation of the QuanInfos values in the psms & peptide tables to words (like in Proteome Discoverer).",
      "topics": [
        "pQuanInfo"
      ]
    },
    {
      "page": "proteinIDTypes",
      "title": "get the names of the identification types (sequest HT etc) used in the database",
      "topics": [
        "proteinIDTypes"
      ]
    },
    {
      "page": "psmAmbiguity",
      "title": "function for 'translation' of the psmAmbiguity values (1..5) in the psmTable to words (like in Proteome Discoverer). <...> -> means not encountered/ undefined/no inference",
      "topics": [
        "psmAmbiguity"
      ]
    },
    {
      "page": "quanInfo",
      "title": "function for 'translation' of the QuanInfo values in the QuanSpectrumInfo table to words (like in Proteome Discoverer).",
      "topics": [
        "quanInfo"
      ]
    },
    {
      "page": "quanInfoDetails",
      "title": "function for 'translation' of the QuanInfoDetails values in the QuanSpectrumInfo table to words (like in Proteome Discoverer).",
      "topics": [
        "quanInfoDetails"
      ]
    },
    {
      "page": "replacementStrings",
      "title": "function that generates the default data.frame for the function df_replace().",
      "topics": [
        "replacementStrings"
      ]
    },
    {
      "page": "SearchInfo",
      "title": "get the table with info on the search itself from the database",
      "topics": [
        "SearchInfo"
      ]
    },
    {
      "page": "spectrum.centroid",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum centroided spectrum",
      "topics": [
        "spectrum.centroid"
      ]
    },
    {
      "page": "spectrum.header",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum header",
      "topics": [
        "spectrum.header"
      ]
    },
    {
      "page": "spectrum.precursor.additionalInfo",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent additonal info",
      "topics": [
        "spectrum.precursor.additionalInfo"
      ]
    },
    {
      "page": "spectrum.precursor.centroid",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent centroided spectrum",
      "topics": [
        "spectrum.precursor.centroid"
      ]
    },
    {
      "page": "spectrum.precursor.header",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent header",
      "topics": [
        "spectrum.precursor.header"
      ]
    },
    {
      "page": "spectrum.precursor.info",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent monoisotopic peak",
      "topics": [
        "spectrum.precursor.info"
      ]
    },
    {
      "page": "spectrum.precursor.profile",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent profile spectrum",
      "topics": [
        "spectrum.precursor.profile"
      ]
    },
    {
      "page": "spectrum.precursor.scanEvent",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent scan event",
      "topics": [
        "spectrum.precursor.scanEvent"
      ]
    },
    {
      "page": "spectrum.profile",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum profile spectrum",
      "topics": [
        "spectrum.profile"
      ]
    },
    {
      "page": "spectrum.scanEvent",
      "title": "gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum scan event",
      "topics": [
        "spectrum.scanEvent"
      ]
    },
    {
      "page": "studyDefinitionExtensions",
      "title": "function that extracts information on isotope corrections (if available)",
      "topics": [
        "studyDefinitionExtensions"
      ]
    },
    {
      "page": "studyDefinitionExtensionSettings",
      "title": "function to extract sample/factor/ratio/replicate information.",
      "topics": [
        "studyDefinitionExtensionSettings"
      ]
    },
    {
      "page": "studyDefinitionFactors",
      "title": "function that extracts the factors used in the study to generate the .pdResult file. The result contains some internal info in the form of columns named id (identifiers).",
      "topics": [
        "studyDefinitionFactors"
      ]
    },
    {
      "page": "studyDefinitionFileSets",
      "title": "function that extracts file information on the original .raw files used to generate the .pdResult file. Information includes the original file name, location & size. It also contains some internal info in the form of columns named id (identifiers).",
      "topics": [
        "studyDefinitionFileSets"
      ]
    },
    {
      "page": "studyDefinitionQuanMethods",
      "title": "function that extracts quantification method information if a quantification method was used to generate the .pdResult file",
      "topics": [
        "studyDefinitionQuanMethods"
      ]
    },
    {
      "page": "studyDefinitionSamples",
      "title": "function that extracts sample information. The information seems to be a bit redundant, as the info is also seen in other tables.",
      "topics": [
        "studyDefinitionSamples"
      ]
    },
    {
      "page": "system.date",
      "title": "converts character string date into date/time format",
      "topics": [
        "system.date"
      ]
    },
    {
      "page": "tableNames",
      "title": "internal helper function to prevent having to remember the somewhat long names of the most used tables",
      "topics": [
        "tableNames"
      ]
    },
    {
      "page": "thermo.date",
      "title": "converts character string date into date/time format",
      "topics": [
        "thermo.date"
      ]
    },
    {
      "page": "tmt10Channels",
      "title": "helper function to generate the a data.frame of TMT knockout strain (TKO) info for other functions. This function generates a data.frame based on the 10-plex TMT TKO knockout (this was the original TMT-knockout-digest available)",
      "topics": [
        "tmt10Channels"
      ]
    },
    {
      "page": "tmt11Channels",
      "title": "helper function to generate the a data.frame of TMT knockout strain (TKO) info for other functions. This function generates a data.frame based on the 11-plex TMT TKO knockout",
      "topics": [
        "tmt11Channels"
      ]
    },
    {
      "page": "totalSearchTime",
      "title": "get the total search time from the database",
      "topics": [
        "totalSearchTime"
      ]
    },
    {
      "page": "transformSpectrumRaw",
      "title": "transforms a spectrum from the table 'MassSpectrumItems' into a R compatible list",
      "topics": [
        "transformSpectrumRaw"
      ]
    },
    {
      "page": "workflowInfo",
      "title": "function to get the workflow information from a .pdResult file",
      "topics": [
        "workflowInfo"
      ]
    }
  ],
  "_readme": "https://github.com/BenBruyneel/proteinDiscover/raw/HEAD/README.md",
  "_rundeps": [
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "DBI",
    "dplyr",
    "fastmap",
    "generics",
    "glue",
    "later",
    "lifecycle",
    "lubridate",
    "magrittr",
    "memoise",
    "pillar",
    "pkgconfig",
    "pool",
    "purrr",
    "R6",
    "Rcpp",
    "rlang",
    "RSQLite",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "utf8",
    "vctrs",
    "withr",
    "XML"
  ],
  "_vignettes": [
    {
      "source": "manual.Rmd",
      "filename": "manual.html",
      "title": "manual",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2022-01-02 14:57:46",
      "modified": "2022-10-15 10:54:59",
      "commits": 2
    }
  ],
  "_score": 3,
  "_indexed": true,
  "_nocasepkg": "proteindiscover",
  "_universes": [
    "benbruyneel"
  ],
  "_binaries": [
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}