Package: LOBSTAHS 1.33.0

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:James Collins [aut, cre], Helen Fredricks [aut], Bethanie Edwards [aut], Henry Holm [aut], Benjamin Van Mooy [aut], Daniel Lowenstein [aut]

LOBSTAHS_1.33.0.tar.gz
LOBSTAHS_1.33.0.zip(r-4.5)LOBSTAHS_1.33.0.zip(r-4.4)LOBSTAHS_1.33.0.zip(r-4.3)
LOBSTAHS_1.33.0.tgz(r-4.4-any)LOBSTAHS_1.33.0.tgz(r-4.3-any)
LOBSTAHS_1.33.0.tar.gz(r-4.5-noble)LOBSTAHS_1.33.0.tar.gz(r-4.4-noble)
LOBSTAHS_1.33.0.tgz(r-4.4-emscripten)LOBSTAHS_1.33.0.tgz(r-4.3-emscripten)
LOBSTAHS.pdf |LOBSTAHS.html✨
LOBSTAHS/json (API)
NEWS

# Install 'LOBSTAHS' in R:
install.packages('LOBSTAHS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/vanmooylipidomics/lobstahs/issues

Datasets:

On BioConductor:LOBSTAHS-1.33.0(bioc 3.21)LOBSTAHS-1.32.0(bioc 3.20)

immunooncologymassspectrometrymetabolomicslipidomicsdataimportadductalgaebioconductorhplc-esi-mslipidmass-spectrometryoxidative-stress-biomarkersoxidized-lipidsoxylipinsplankton

6.56 score 8 stars 9 scripts 245 downloads 5 mentions 49 exports 151 dependencies

Last updated 2 months agofrom:39dadf2e6f. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 27 2024
R-4.5-winWARNINGNov 27 2024
R-4.5-linuxWARNINGNov 27 2024
R-4.4-winWARNINGNov 27 2024
R-4.4-macWARNINGNov 27 2024
R-4.3-winWARNINGNov 27 2024
R-4.3-macWARNINGNov 27 2024

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:abindaffyaffyioAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemCAMERAcheckmatecliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmennetopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRBGLRColorBrewerRcppreshape2Rhdf5librlangrmarkdownrpartrstudioapiS4ArraysS4VectorssassscalessnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisviridisLitevsnwithrxcmsxfunXMLXVectoryamlzlibbioc

Discovery, Identification, and Screening of Lipids and Oxylipins in HPLC-MS Datasets Using LOBSTAHS

James Collins

Rendered fromLOBSTAHS.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2021-08-30
Started: 2016-07-05

Readme and manuals

Help Manual

Help pageTopics
Screen, annotate, and identify compounds in an xsAnnotate objectdoLOBscreen
Export a LOBSTAHS database (LOBdbase) object to a text fileexportDBtoCSV
Extract compound data from a LOBdbaseextractLOBdbasedata
Conduct _in silico_ simulation and generate lipid-oxylipin databasegenerateLOBdbase
Export screened LOBSTAHS peaklist with compound assignmentsgetLOBpeaklist
Import and reconstruct LOBdbase from a text fileloadLOBdbase
LOBdbase constructor for manual creation or reconstruction of a LOBdbase objectLOBdbase
Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databasesadduct 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 parametersdefault.acylRanges default.adductHierarchies default.componentCompTable default.LOBdbase default.oxyRanges default.rt.windows LOBdefaults
LOBSet constructor for manual creation or reconstruction of a LOBSet objectLOBSet
Class LOBSet: Peak data with annotations, isomers, and compound assignmentsLOBisoID_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