# Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

## Documentation for package ‘LOBSTAHS’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A D E F G L M N P S

## -- A --

adduct | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
adduct-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
adduct<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
adduct<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
adduct_rank | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
adduct_rank-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
adduct_rank<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
adduct_rank<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases

## -- D --

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
degree_oxidation | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
degree_oxidation-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
degree_oxidation<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
degree_oxidation<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
doLOBscreen | Screen, annotate, and identify compounds in an xsAnnotate object

## -- E --

exact_parent_neutral_mass | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
exact_parent_neutral_mass-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
exact_parent_neutral_mass<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
exact_parent_neutral_mass<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
exportDBtoCSV | Export a LOBSTAHS database (LOBdbase) object to a text file
extractLOBdbasedata | Extract compound data from a LOBdbase

## -- F --

FA_total_no_C | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
FA_total_no_C-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
FA_total_no_C<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
FA_total_no_C<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
FA_total_no_DB | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
FA_total_no_DB-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
FA_total_no_DB<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
FA_total_no_DB<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
frag_ID | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
frag_ID-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
frag_ID<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
frag_ID<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases

## -- G --

generateLOBdbase | Conduct _in silico_ simulation and generate lipid-oxylipin database
getLOBpeaklist | Export screened LOBSTAHS peaklist with compound assignments

## -- L --

lipid_class | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
lipid_class-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
lipid_class<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
lipid_class<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
loadLOBdbase | Import and reconstruct LOBdbase from a text file
LOBdbase | LOBdbase constructor for manual creation or reconstruction of a LOBdbase object
LOBdbase-class | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
LOBdefaults | LOBSTAHS default databases and database generation parameters
LOBisoID_diagnostics | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBisoID_diagnostics-method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBisoID_diagnostics<- | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBisoID_diagnostics<--method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBscreen_diagnostics | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBscreen_diagnostics-method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBscreen_diagnostics<- | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBscreen_diagnostics<--method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBscreen_settings | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBscreen_settings-method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBscreen_settings<- | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBscreen_settings<--method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
LOBSet | LOBSet constructor for manual creation or reconstruction of a LOBSet object
LOBSet-class | Class LOBSet: Peak data with annotations, isomers, and compound assignments

## -- M --

mz | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
mz-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
mz<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
mz<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases

## -- N --

num_compounds | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
num_compounds-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
num_compounds<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
num_compounds<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
num_entries | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
num_entries-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
num_entries<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
num_entries<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases

## -- P --

parent_compound_name | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
parent_compound_name-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
parent_compound_name<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
parent_compound_name<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
parent_elem_formula | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
parent_elem_formula-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
parent_elem_formula<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
parent_elem_formula<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
peakdata | Class LOBSet: Peak data with annotations, isomers, and compound assignments
peakdata-method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
peakdata<- | Class LOBSet: Peak data with annotations, isomers, and compound assignments
peakdata<--method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
polarity | Class LOBSet: Peak data with annotations, isomers, and compound assignments
polarity-method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
polarity-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
polarity<- | Class LOBSet: Peak data with annotations, isomers, and compound assignments
polarity<--method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
polarity<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases

## -- S --

sampnames | Class LOBSet: Peak data with annotations, isomers, and compound assignments
sampnames-method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
sampnames<- | Class LOBSet: Peak data with annotations, isomers, and compound assignments
sampnames<--method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
show-method | Class LOBSet: Peak data with annotations, isomers, and compound assignments
show-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
species | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
species-method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
species<- | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
species<--method | Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases