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.

AuthorJames Collins [aut, cre], Helen Fredricks [aut], Bethanie Edwards [aut], Benjamin Van Mooy [aut]
Date of publicationNone
MaintainerJames Collins <james.r.collins@aya.yale.edu>
LicenseGPL (>= 3) + file LICENSE
Version1.0.0
http://bioconductor.org/packages/LOBSTAHS

View on Bioconductor

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

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