Package: proteinDiscover 0.11.0

proteinDiscover: ProteinDiscover

Provides an interface to the data contained in Proteome Discoverer (Thermo Scientific) results.

Authors:Ben Bruyneel <[email protected]>

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
proteinDiscover/json (API)

# Install 'proteinDiscover' in R:

install.packages('proteinDiscover', repos = c('https://benbruyneel.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/benbruyneel/proteindiscover/issues

On CRAN:

mass-spectrometry proteomics proteomics-data-analysis

3.00 score 2 stars 2 scripts 82 exports 34 dependencies

Last updated from:04b6e22d41. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	132
source / vignettes	OK	215
linux-release	OK	131
macos-release	OK	204
macos-oldrel	OK	236
windows-devel	OK	94
windows-release	OK	96
windows-oldrel	OK	90
wasm-release	OK	94

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

Dependencies: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

manual

Rendered frommanual.Rmdusingknitr::rmarkdown

Last update: 2022-10-15
Started: 2022-01-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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	allNodesTable
function that gets the first element of the AnalysisDefinitionXML column from the AnalysisDefinition table in a .pdResult file	analysisDefinition
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	blobLength
Wrapper function that uses 'tmt11Channels' to calculate the IFI's for a set of (knock out) protein channels	calcAllIFIs
helper function to calculate a row-wise function (like mean, median etc) across a data.frame	calcData
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	calcIFIs
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	columnSpecials
function to create a DiagrammeR string that can be used by DiagrammeR::grViz() to plot a visual representation of the workflow	createDiagrammeRString
Wrapper around pool::pooClose(): closes an open database (normally opened earlier via eg db_open())	dbClose
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'	dbGetAnnotatedProteins
Function to get the info for (protein) annotation groups. Takes eg 'dbGetProteinAnnotationGroupIDs' as input	dbGetAnnotationGroups
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'	dbGetAnnotationGroupsFiltered
get the ConsensusID's from (a set of) PeptideGroupIDs	dbGetConsensusIDs
get the Consensus Features table belonging to the ConsensusIDs	dbGetConsensusTable
get the MassSpectrumItems info from (a set of) PeptideID's	dbGetMassSpectrumItems
Function to get the peptideID's 'belonging' to a modification site	dbGetModificationPeptideIDs
function to get the modificationSite ID's from (a set of) proteinUniqueID's	dbGetModificationsSitesIDs
function to get data from the ModificationSides table using the modificiationSiteId's	dbGetModificationsTable
get the MSnSpectrumInfo from (a set of) PeptideID's	dbGetMSnSpectrumInfo
get the peptideID's from (a set of) proteinGroupIDs	dbGetPeptideIDs
get the paptide table belonging defined by PeptideIDs ot proteinGroupIDs	dbGetPeptideTable
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'	dbGetProteinAnnotationGroupIDs
A bit more advanced version of 'dbGetProteinTable' which allows for filtering (via SQL). Note that filtering raw columns (BLOB's) will not work properly	dbGetProteinFiltered
Retrieve the ProteinGroupID's of proteins via their UniqueSequenceID's	dbGetProteinGroupIDs
Gets the ProteinGroup information from the TargetProteinGroups table	dbGetProteinGroups
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	dbGetProteinIDs
Function to get protein information from the TargetProteins table on the basis of their UniqueSequenceID	dbGetProteins
get the protein table from a .pdResult file (essentially a wrapper around db_getTable())	dbGetProteinTable
Function to retrieve the UniqueSequenceID's based on the accession field of the proteinTable. Essentially a wrapper for 'dbGetProteinFiltered'	dbGetProteinUniqueSequenceIDs
get the PsmID's from (a set of) PeptideGroupIDs	dbGetPsmIDs
get the PSM table belonging to the PsmIDs	dbGetPsmTable
get the SpectrumID's from (a set of) PeptideIDs	dbGetQuanSpectrumIDs
get the QuanSpectrumInfo table belonging to the SpectrumID's	dbGetQuanSpectrumInfoTable
get a table from a .pdResult file	dbGetTable
Wrapper around pool::dbPool(): opens a database	dbOpen
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	determineBlobTypes
function that replaces (parts of) strings in a data.frame according to a provided table of replacements	df_replace
df_transform_raws(): converts raw columns in a data.frame to the correct data types	dfTransformRaws
function to retrieve the acquisition date of the files used to generate the pdResult file	getAcquistionDate
function to retrieve the acquisition date & time of the files used to generate the pdResult file	getAcquistionDateTime
detemines which columns in a table are of the blob (raw) type	getBlobs
get peptide information from the peptide table from a pdResult file based on the provided proteinAccession (uniprot) codes. Raw columns are "translated"	getPeptideInfo
get peptide information from the peptide table from a pdResult file based on the provided proteinAccession (uniprot) codes. Raw columns are not "translated"	getPeptideInfoRaw
get protein info (with translation of columns) from a list of protein Accessions (uniprot code). Essentially this is a wrapper function for 'getProteinInfoRaw'	getProteinInfo
get protein info (without translation of columns) from a list of protein Accessions (uniprot code). Essentially this is a wrapper function for 'dbGetTable'	getProteinInfoRaw
function for 'translation' of the isMasterProtein values (0..4) in the proteinTable to words (like in Proteome Discoverer).	isMasterProtein
helper function to generate the a data.frame of proteins info for other functions	knockOutProteins
get the table with info on the files used in the search from the database	MSfileInfo
fake converter for times when no conversion is wanted/needed	na.date
function that takes a (xmlToList type) workflow and returns a list of nodes	nodes
function to display an overview table of the processing/consensus workflows in the nodeInfo coming out of the workflowInfo function	nodeTable
function for translation of the QuanInfos values in the psms & peptide tables to words (like in Proteome Discoverer).	pQuanInfo
get the names of the identification types (sequest HT etc) used in the database	proteinIDTypes
function for 'translation' of the psmAmbiguity values (1..5) in the psmTable to words (like in Proteome Discoverer). <...> -> means not encountered/ undefined/no inference	psmAmbiguity
function for 'translation' of the QuanInfo values in the QuanSpectrumInfo table to words (like in Proteome Discoverer).	quanInfo
function for 'translation' of the QuanInfoDetails values in the QuanSpectrumInfo table to words (like in Proteome Discoverer).	quanInfoDetails
function that generates the default data.frame for the function df_replace().	replacementStrings
get the table with info on the search itself from the database	SearchInfo
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum centroided spectrum	spectrum.centroid
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum header	spectrum.header
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent additonal info	spectrum.precursor.additionalInfo
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent centroided spectrum	spectrum.precursor.centroid
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent header	spectrum.precursor.header
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent monoisotopic peak	spectrum.precursor.info
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent profile spectrum	spectrum.precursor.profile
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum parent scan event	spectrum.precursor.scanEvent
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum profile spectrum	spectrum.profile
gets the info in the list object coming from the function 'transformSpectrumRaw': spectrum scan event	spectrum.scanEvent
function that extracts information on isotope corrections (if available)	studyDefinitionExtensions
function to extract sample/factor/ratio/replicate information.	studyDefinitionExtensionSettings
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).	studyDefinitionFactors
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).	studyDefinitionFileSets
function that extracts quantification method information if a quantification method was used to generate the .pdResult file	studyDefinitionQuanMethods
function that extracts sample information. The information seems to be a bit redundant, as the info is also seen in other tables.	studyDefinitionSamples
converts character string date into date/time format	system.date
internal helper function to prevent having to remember the somewhat long names of the most used tables	tableNames
converts character string date into date/time format	thermo.date
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)	tmt10Channels
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	tmt11Channels
get the total search time from the database	totalSearchTime
transforms a spectrum from the table 'MassSpectrumItems' into a R compatible list	transformSpectrumRaw
function to get the workflow information from a .pdResult file	workflowInfo