Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences


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Documentation for package ‘LOBSTAHS’ version 1.30.0

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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