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.

Author
James Collins [aut, cre], Helen Fredricks [aut], Bethanie Edwards [aut], Benjamin Van Mooy [aut]
Date of publication
None
Maintainer
James Collins <james.r.collins@aya.yale.edu>
License
GPL (>= 3) + file LICENSE
Version
1.0.0
URLs

View on Bioconductor

Man pages

doLOBscreen
Screen, annotate, and identify compounds in an xsAnnotate...
extractLOBdbasedata
Extract compound data from a LOBdbase
generateLOBdbase
Conduct _in silico_ simulation and generate lipid-oxylipin...
getLOBpeaklist
Export screened LOBSTAHS peaklist with compound assignments
loadLOBdbase
Import and reconstruct LOBdbase from a text file
LOBdbase
LOBdbase constructor for manual creation or reconstruction of...
LOBdbase-class
Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
LOBdefaults
LOBSTAHS default databases and database generation parameters
LOBSet
LOBSet constructor for manual creation or reconstruction of a...
LOBSet-class
Class LOBSet: Peak data with annotations, isomers, and...

Files in this package

LOBSTAHS/.BBSoptions
LOBSTAHS/DESCRIPTION
LOBSTAHS/LICENSE
LOBSTAHS/NAMESPACE
LOBSTAHS/R
LOBSTAHS/R/LOBSet.R
LOBSTAHS/R/LOBdbase.R
LOBSTAHS/R/doLOBscreen.R
LOBSTAHS/R/generateLOBdbase.R
LOBSTAHS/README.md
LOBSTAHS/build
LOBSTAHS/build/vignette.rds
LOBSTAHS/data
LOBSTAHS/data/datalist
LOBSTAHS/data/default.LOBdbase.RData
LOBSTAHS/data/default.acylRanges.RData
LOBSTAHS/data/default.adductHierarchies.RData
LOBSTAHS/data/default.componentCompTable.RData
LOBSTAHS/data/default.oxyRanges.RData
LOBSTAHS/data/default.rt.windows.RData
LOBSTAHS/inst
LOBSTAHS/inst/CITATION
LOBSTAHS/inst/NEWS
LOBSTAHS/inst/doc
LOBSTAHS/inst/doc/LOBSTAHS.R
LOBSTAHS/inst/doc/LOBSTAHS.Rmd
LOBSTAHS/inst/doc/LOBSTAHS.html
LOBSTAHS/inst/doc/csv
LOBSTAHS/inst/doc/csv/LOBSTAHS_acyl_prop_ranges.csv
LOBSTAHS/inst/doc/csv/LOBSTAHS_addl_oxy_ranges.csv
LOBSTAHS/inst/doc/csv/LOBSTAHS_adduct_ion_hierarchies.csv
LOBSTAHS/inst/doc/csv/LOBSTAHS_basic_component_matrix.csv
LOBSTAHS/inst/doc/csv/LOBSTAHS_lipid_class_rt_windows.csv
LOBSTAHS/inst/doc/xlsx
LOBSTAHS/inst/doc/xlsx/LOBSTAHS_acyl_prop_ranges.xlsx
LOBSTAHS/inst/doc/xlsx/LOBSTAHS_addl_oxy_ranges.xlsx
LOBSTAHS/inst/doc/xlsx/LOBSTAHS_adduct_ion_hierarchies.xlsx
LOBSTAHS/inst/doc/xlsx/LOBSTAHS_basic_component_matrix.xlsx
LOBSTAHS/inst/doc/xlsx/LOBSTAHS_lipid_class_rt_windows.xlsx
LOBSTAHS/man
LOBSTAHS/man/LOBSet-class.Rd
LOBSTAHS/man/LOBSet.Rd
LOBSTAHS/man/LOBdbase-class.Rd
LOBSTAHS/man/LOBdbase.Rd
LOBSTAHS/man/LOBdefaults.Rd
LOBSTAHS/man/doLOBscreen.Rd
LOBSTAHS/man/extractLOBdbasedata.Rd
LOBSTAHS/man/generateLOBdbase.Rd
LOBSTAHS/man/getLOBpeaklist.Rd
LOBSTAHS/man/loadLOBdbase.Rd
LOBSTAHS/vignettes
LOBSTAHS/vignettes/LOBSTAHS.Rmd
LOBSTAHS/vignettes/images
LOBSTAHS/vignettes/images/Fig1.jpg