Introduction | Purpose | Installing the LOBSTAHS package | Install current production version | Install "no warranties" development version with latest features | Install dependencies: | Install RTools: | Install packages needed for installation from Github: | Install LOBSTAHS: | Install 'PtH2O2lipids,' containing example data & precursor xsAnnotate object: | "Operating instructions," part 1: Pre-processing | Acquisition of HPLC-MS data suitable for LOBSTAHS | File conversion | Initial file conversion; saves converted file to a directory "mzXML_ms1_two_mode": | Extract positive, negative mode scans, then save in separate directories: | Pre-processing with xcms | Final pre-processing with CAMERA | "Operating instructions," part 2: The LOBSTAHS databases | A note about molecular diversity in the current databases | Accessing the default databases | Concept of operation: Using input tables | Introduction to the four input tables | The componentCompTable | The acylRanges and oxyRanges tables | The adductHierarchies table | Modification of table data to create new database entries | First scenario: Defining single compounds | Second scenario: Defining entire lipid classes for which an iterative simulation is to be performed | Saving of files | Database generation using generateLOBdbase | "Operating instructions," part 3: Compound/biomarker identification and screening using doLOBscreen (or, the "meat" of LOBSTAHS) | Follow-on analysis of screened data | Package updates and improvements | Copyright | References | Notes
Package: LOBSTAHS 1.39.0
Henry Holm
LOBSTAHS: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.
Authors:
LOBSTAHS_1.39.0.tar.gz
LOBSTAHS_1.39.0.zip(r-4.7)LOBSTAHS_1.39.0.zip(r-4.6)LOBSTAHS_1.39.0.zip(r-4.5)
LOBSTAHS_1.39.0.tgz(r-4.6-any)LOBSTAHS_1.39.0.tgz(r-4.5-any)
LOBSTAHS_1.39.0.tar.gz(r-4.7-any)LOBSTAHS_1.39.0.tar.gz(r-4.6-any)
LOBSTAHS_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LOBSTAHS/json (API)
| # Install 'LOBSTAHS' in R: |
| install.packages('LOBSTAHS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/vanmooylipidomics/lobstahs/issues
Datasets:
- default.acylRanges - LOBSTAHS default databases and database generation parameters
- default.adductHierarchies - LOBSTAHS default databases and database generation parameters
- default.componentCompTable - LOBSTAHS default databases and database generation parameters
- default.LOBdbase - LOBSTAHS default databases and database generation parameters
- default.oxyRanges - LOBSTAHS default databases and database generation parameters
- default.rt.windows - LOBSTAHS default databases and database generation parameters
On BioConductor:LOBSTAHS-1.39.0(bioc 3.24)LOBSTAHS-1.38.0(bioc 3.23)
immunooncologymassspectrometrymetabolomicslipidomicsdataimportadductalgaebioconductorhplc-esi-mslipidmass-spectrometryoxidative-stress-biomarkersoxidized-lipidsoxylipinsplankton
Last updated from:2f45bdb3b2. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 250 | ||
| linux-devel-x86_64 | NOTE | 479 | ||
| source / vignettes | OK | 383 | ||
| linux-release-x86_64 | NOTE | 479 | ||
| macos-release-arm64 | NOTE | 266 | ||
| macos-oldrel-arm64 | NOTE | 250 | ||
| windows-devel | NOTE | 479 | ||
| windows-release | NOTE | 456 | ||
| windows-oldrel | NOTE | 412 | ||
| wasm-release | OK | 241 |
Exports:adductadduct_rankadduct_rank<-adduct<-degree_oxidationdegree_oxidation<-doLOBscreenexact_parent_neutral_massexact_parent_neutral_mass<-exportDBtoCSVextractLOBdbasedataFA_total_no_CFA_total_no_C<-FA_total_no_DBFA_total_no_DB<-frag_IDfrag_ID<-generateLOBdbasegetLOBpeaklistlipid_classlipid_class<-loadLOBdbaseLOBdbaseLOBisoID_diagnosticsLOBisoID_diagnostics<-LOBscreen_diagnosticsLOBscreen_diagnostics<-LOBscreen_settingsLOBscreen_settings<-LOBSetmzmz<-num_compoundsnum_compounds<-num_entriesnum_entries<-parent_compound_nameparent_compound_name<-parent_elem_formulaparent_elem_formula<-peakdatapeakdata<-polaritypolarity<-sampnamessampnames<-showspeciesspecies<-
Dependencies:abindaffyaffyioAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbslibcachemCAMERAcheckmatecliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4nnetopensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRBGLRColorBrewerRcppreshape2Rhdf5librlangrmarkdownrpartrstudioapiS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Screen, annotate, and identify compounds in an xsAnnotate object | doLOBscreen |
| Export a LOBSTAHS database (LOBdbase) object to a text file | exportDBtoCSV |
| Extract compound data from a LOBdbase | extractLOBdbasedata |
| Conduct _in silico_ simulation and generate lipid-oxylipin database | generateLOBdbase |
| Export screened LOBSTAHS peaklist with compound assignments | getLOBpeaklist |
| Import and reconstruct LOBdbase from a text file | loadLOBdbase |
| LOBdbase constructor for manual creation or reconstruction of a LOBdbase object | LOBdbase |
| Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases | adduct adduct,LOBdbase-method adduct<- adduct<-,LOBdbase-method adduct_rank adduct_rank,LOBdbase-method adduct_rank<- adduct_rank<-,LOBdbase-method degree_oxidation degree_oxidation,LOBdbase-method degree_oxidation<- degree_oxidation<-,LOBdbase-method exact_parent_neutral_mass exact_parent_neutral_mass,LOBdbase-method exact_parent_neutral_mass<- exact_parent_neutral_mass<-,LOBdbase-method FA_total_no_C FA_total_no_C,LOBdbase-method FA_total_no_C<- FA_total_no_C<-,LOBdbase-method FA_total_no_DB FA_total_no_DB,LOBdbase-method FA_total_no_DB<- FA_total_no_DB<-,LOBdbase-method frag_ID frag_ID,LOBdbase-method frag_ID<- frag_ID<-,LOBdbase-method lipid_class lipid_class,LOBdbase-method lipid_class<- lipid_class<-,LOBdbase-method LOBdbase-class mz mz,LOBdbase-method mz<- mz<-,LOBdbase-method num_compounds num_compounds,LOBdbase-method num_compounds<- num_compounds<-,LOBdbase-method num_entries num_entries,LOBdbase-method num_entries<- num_entries<-,LOBdbase-method parent_compound_name parent_compound_name,LOBdbase-method parent_compound_name<- parent_compound_name<-,LOBdbase-method parent_elem_formula parent_elem_formula,LOBdbase-method parent_elem_formula<- parent_elem_formula<-,LOBdbase-method polarity,LOBdbase-method polarity<-,LOBdbase-method show,LOBdbase-method species species,LOBdbase-method species<- species<-,LOBdbase-method |
| LOBSTAHS default databases and database generation parameters | default.acylRanges default.adductHierarchies default.componentCompTable default.LOBdbase default.oxyRanges default.rt.windows LOBdefaults |
| LOBSet constructor for manual creation or reconstruction of a LOBSet object | LOBSet |
| Class LOBSet: Peak data with annotations, isomers, and compound assignments | LOBisoID_diagnostics LOBisoID_diagnostics,LOBSet-method LOBisoID_diagnostics<- LOBisoID_diagnostics<-,LOBSet-method LOBscreen_diagnostics LOBscreen_diagnostics,LOBSet-method LOBscreen_diagnostics<- LOBscreen_diagnostics<-,LOBSet-method LOBscreen_settings LOBscreen_settings,LOBSet-method LOBscreen_settings<- LOBscreen_settings<-,LOBSet-method LOBSet-class peakdata peakdata,LOBSet-method peakdata<- peakdata<-,LOBSet-method polarity polarity,LOBSet-method polarity<- polarity<-,LOBSet-method sampnames sampnames,LOBSet-method sampnames<- sampnames<-,LOBSet-method show,LOBSet-method |
