Man pages for BenBruyneel/proteinDiscover
ProteinDiscover
| allNodesTable | Helper function that takes the result from the 'nodes'... |
| analysisDefinition | function that gets the first element of the... |
| blobLength | attempts to determine the length (in bytes) of the individual... |
| calcAllIFIs | Wrapper function that uses 'tmt11Channels' to calculate the... |
| calcData | helper function to calculate a row-wise function (like mean,... |
| calcIFIs | function to calculate the IFI (interference free index) of a... |
| columnSpecials | Specials are not numeric or integer, but have chunks of a... |
| createDiagrammeRString | function to create a DiagrammeR string that can be used by... |
| dbClose | Wrapper around pool::pooClose(): closes an open database... |
| dbGetAnnotatedProteins | Function to get the UniqueSequenceID's for proteins which are... |
| dbGetAnnotationGroups | Function to get the info for (protein) annotation groups.... |
| dbGetAnnotationGroupsFiltered | Get Group Annotation information from the table:... |
| dbGetConsensusIDs | get the ConsensusID's from (a set of) PeptideGroupIDs |
| dbGetConsensusTable | get the Consensus Features table belonging to the... |
| dbGetMassSpectrumItems | get the MassSpectrumItems info from (a set of) PeptideID's |
| dbGetModificationPeptideIDs | Function to get the peptideID's 'belonging' to a modification... |
| dbGetModificationsSitesIDs | function to get the modificationSite ID's from (a set of)... |
| dbGetModificationsTable | function to get data from the ModificationSides table using... |
| dbGetMSnSpectrumInfo | get the MSnSpectrumInfo from (a set of) PeptideID's |
| dbGetPeptideIDs | get the peptideID's from (a set of) proteinGroupIDs |
| dbGetPeptideTable | get the paptide table belonging defined by PeptideIDs ot... |
| dbGetProteinAnnotationGroupIDs | Function to get the functional group annotation group ID's... |
| dbGetProteinFiltered | A bit more advanced version of 'dbGetProteinTable' which... |
| dbGetProteinGroupIDs | Retrieve the ProteinGroupID's of proteins via their... |
| dbGetProteinGroups | Gets the ProteinGroup information from the... |
| dbGetProteinIDs | Function to get proteinUniqueID's from a (set of) protein... |
| dbGetProteins | Function to get protein information from the TargetProteins... |
| dbGetProteinTable | get the protein table from a .pdResult file (essentially a... |
| dbGetProteinUniqueSequenceIDs | Function to retrieve the UniqueSequenceID's based on the... |
| dbGetPsmIDs | get the PsmID's from (a set of) PeptideGroupIDs |
| dbGetPsmTable | get the PSM table belonging to the PsmIDs |
| dbGetQuanSpectrumIDs | get the SpectrumID's from (a set of) PeptideIDs |
| dbGetQuanSpectrumInfoTable | get the QuanSpectrumInfo table belonging to the SpectrumID's |
| dbGetTable | get a table from a .pdResult file |
| dbOpen | Wrapper around pool::dbPool(): opens a database |
| determineBlobTypes | function that attempts to assign types and sizes to the blob... |
| df_replace | function that replaces (parts of) strings in a data.frame... |
| dfTransformRaws | df_transform_raws(): converts raw columns in a data.frame to... |
| getAcquistionDate | function to retrieve the acquisition date of the files used... |
| getAcquistionDateTime | function to retrieve the acquisition date & time of the files... |
| getBlobs | detemines which columns in a table are of the blob (raw) type |
| getPeptideInfo | get peptide information from the peptide table from a... |
| getPeptideInfoRaw | get peptide information from the peptide table from a... |
| getProteinInfo | get protein info (with translation of columns) from a list of... |
| getProteinInfoRaw | get protein info (without translation of columns) from a list... |
| isMasterProtein | function for 'translation' of the isMasterProtein values... |
| knockOutProteins | helper function to generate the a data.frame of proteins info... |
| MSfileInfo | get the table with info on the files used in the search from... |
| na.date | fake converter for times when no conversion is wanted/needed |
| nodes | function that takes a (xmlToList type) workflow and returns a... |
| nodeTable | function to display an overview table of the... |
| pQuanInfo | function for translation of the QuanInfos values in the psms... |
| proteinIDTypes | get the names of the identification types (sequest HT etc)... |
| psmAmbiguity | function for 'translation' of the psmAmbiguity values (1..5)... |
| quanInfo | function for 'translation' of the QuanInfo values in the... |
| quanInfoDetails | function for 'translation' of the QuanInfoDetails values in... |
| replacementStrings | function that generates the default data.frame for the... |
| SearchInfo | get the table with info on the search itself from the... |
| spectrum.centroid | gets the info in the list object coming from the function... |
| spectrum.header | gets the info in the list object coming from the function... |
| spectrum.precursor.additionalInfo | gets the info in the list object coming from the function... |
| spectrum.precursor.centroid | gets the info in the list object coming from the function... |
| spectrum.precursor.header | gets the info in the list object coming from the function... |
| spectrum.precursor.info | gets the info in the list object coming from the function... |
| spectrum.precursor.profile | gets the info in the list object coming from the function... |
| spectrum.precursor.scanEvent | gets the info in the list object coming from the function... |
| spectrum.profile | gets the info in the list object coming from the function... |
| spectrum.scanEvent | gets the info in the list object coming from the function... |
| studyDefinitionExtensions | function that extracts information on isotope corrections (if... |
| studyDefinitionExtensionSettings | function to extract sample/factor/ratio/replicate... |
| studyDefinitionFactors | function that extracts the factors used in the study to... |
| studyDefinitionFileSets | function that extracts file information on the original .raw... |
| studyDefinitionQuanMethods | function that extracts quantification method information if a... |
| studyDefinitionSamples | function that extracts sample information. The information... |
| system.date | converts character string date into date/time format |
| tableNames | internal helper function to prevent having to remember the... |
| thermo.date | converts character string date into date/time format |
| tmt10Channels | helper function to generate the a data.frame of TMT knockout... |
| tmt11Channels | helper function to generate the a data.frame of TMT knockout... |
| totalSearchTime | get the total search time from the database |
| transformSpectrumRaw | transforms a spectrum from the table 'MassSpectrumItems' into... |
| workflowInfo | function to get the workflow information from a .pdResult... |
