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

Functions

adduct Man page
adduct<- Man page
adduct<-,LOBdbase-method Man page
adduct,LOBdbase-method Man page
adduct_rank Man page
adduct_rank<- Man page
adduct_rank<-,LOBdbase-method Man page
adduct_rank,LOBdbase-method Man page
default.acylRanges Man page
default.adductHierarchies Man page
default.componentCompTable Man page
default.LOBdbase Man page
default.oxyRanges Man page
default.rt.windows Man page
degree_oxidation Man page
degree_oxidation<- Man page
degree_oxidation<-,LOBdbase-method Man page
degree_oxidation,LOBdbase-method Man page
doLOBscreen Man page
exact_parent_neutral_mass Man page
exact_parent_neutral_mass<- Man page
exact_parent_neutral_mass<-,LOBdbase-method Man page
exact_parent_neutral_mass,LOBdbase-method Man page
extractLOBdbasedata Man page
FA_total_no_C Man page
FA_total_no_C<- Man page
FA_total_no_C<-,LOBdbase-method Man page
FA_total_no_C,LOBdbase-method Man page
FA_total_no_DB Man page
FA_total_no_DB<- Man page
FA_total_no_DB<-,LOBdbase-method Man page
FA_total_no_DB,LOBdbase-method Man page
frag_ID Man page
frag_ID<- Man page
frag_ID<-,LOBdbase-method Man page
frag_ID,LOBdbase-method Man page
generateLOBdbase Man page
getLOBpeaklist Man page
lipid_class Man page
lipid_class<- Man page
lipid_class<-,LOBdbase-method Man page
lipid_class,LOBdbase-method Man page
loadLOBdbase Man page
LOBdbase Man page
LOBdbase-class Man page
LOBdefaults Man page
LOBisoID_diagnostics Man page
LOBisoID_diagnostics<- Man page
LOBisoID_diagnostics<-,LOBSet-method Man page
LOBisoID_diagnostics,LOBSet-method Man page
LOBscreen_diagnostics Man page
LOBscreen_diagnostics<- Man page
LOBscreen_diagnostics<-,LOBSet-method Man page
LOBscreen_diagnostics,LOBSet-method Man page
LOBscreen_settings Man page
LOBscreen_settings<- Man page
LOBscreen_settings<-,LOBSet-method Man page
LOBscreen_settings,LOBSet-method Man page
LOBSet Man page
LOBSet-class Man page
mz Man page
mz<- Man page
mz<-,LOBdbase-method Man page
mz,LOBdbase-method Man page
num_compounds Man page
num_compounds<- Man page
num_compounds<-,LOBdbase-method Man page
num_compounds,LOBdbase-method Man page
num_entries Man page
num_entries<- Man page
num_entries<-,LOBdbase-method Man page
num_entries,LOBdbase-method Man page
parent_compound_name Man page
parent_compound_name<- Man page
parent_compound_name<-,LOBdbase-method Man page
parent_compound_name,LOBdbase-method Man page
parent_elem_formula Man page
parent_elem_formula<- Man page
parent_elem_formula<-,LOBdbase-method Man page
parent_elem_formula,LOBdbase-method Man page
peakdata Man page
peakdata<- Man page
peakdata<-,LOBSet-method Man page
peakdata,LOBSet-method Man page
polarity Man page
polarity<- Man page
polarity<-,LOBdbase-method Man page
polarity,LOBdbase-method Man page
polarity<-,LOBSet-method Man page
polarity,LOBSet-method Man page
sampnames Man page
sampnames<- Man page
sampnames<-,LOBSet-method Man page
sampnames,LOBSet-method Man page
show,LOBdbase-method Man page
show,LOBSet-method Man page
species Man page
species<- Man page
species<-,LOBdbase-method Man page
species,LOBdbase-method Man page

Files

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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