LOBdbase-class: Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases

In hholm/LOBSTAHS: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases

Description

A class for LOBSTAHS databases that contain a combination of in silico and empirical data for a wide range of lipids, oxidized lipids, and oxylipins.

Objects from the class

Objects can be created using the simulation function generateLOBdbase (preferred; satisfies the needs of most users), imported from a .csv file of proper format using loadLOBdbase, or created using the rudimentary constructor LOBdbase (least preferred). A 'LOBdbase' can also be created by calls of the form new("LOBdbase", ...).

Slots

frag_ID:

Object of class "integer", a unique identifier for this molecular species

mz:

Object of class "numeric", the calculated m/z of this species

exact_parent_neutral_mass:

Object of class "numeric", the calculated (monoisotopic) exact mass of the parent compound of this species

lipid_class:

Object of class "factor", the parent lipid class of this species

species:

Object of class "character", the lipid subclass

adduct:

Object of class "factor", the adduct ion represented by this entry

adduct_rank:

Object of class "integer", the relative abundance ranking of this adduct relative to the other adducts of the same parent compound

FA_total_no_C:

Object of class "integer", total number of acyl (fatty acid) carbon atoms in the parent compound; NA if lipid_class is not TAG, IP-DAG, PUA, or FFA

FA_total_no_DB:

Object of class "integer", total number of acyl (fatty acid) carbon-carbon double bonds in the parent compound; NA if lipid_class is not TAG, IP-DAG, PUA, or FFA

degree_oxidation:

Object of class "integer", number of additional oxygen atoms present

parent_elem_formula:

Object of class "character", elemental formula of the parent compound

parent_compound_name:

Object of class "character", name of the parent compound; see the reference for this entry for the naming convention applied to compounds other than pigments

polarity:

Object of class "factor", ionization mode of data in the database

num_entries:

Object of class "integer", number of total entries (adducts) in the database

num_compounds:

Object of class "integer", number of parent compounds represented in the database (should be < num_entries)

Methods

show

signature(object = "LOBdbase"): ...

polarity

signature(object = "LOBdbase"): get polarity slot

num_compounds

signature(object = "LOBdbase"): get num_compounds slot

num_entries

signature(object = "LOBdbase"): get num_entries slot

frag_ID

signature(object = "LOBdbase"): get frag_ID slot

exact_parent_neutral_mass

signature(object = "LOBdbase"): get exact_parent_neutral_mass slot

lipid_class

signature(object = "LOBdbase"): get lipid_class slot

species

signature(object = "LOBdbase"): get species slot

adduct

signature(object = "LOBdbase"): get adduct slot

adduct_rank

signature(object = "LOBdbase"): get adduct_rank slot

FA_total_no_C

signature(object = "LOBdbase"): get FA_total_no_C slot

FA_total_no_DB

signature(object = "LOBdbase"): get FA_total_no_DB slot

degree_oxidation

signature(object = "LOBdbase"): get degree_oxidation slot

parent_elem_formula

signature(object = "LOBdbase"): get parent_elem_formula slot

parent_compound_name

signature(object = "LOBdbase"): get parent_compound_name slot

Author(s)

James Collins, [e-mail]

References

Collins, J.R., B.R. Edwards, H.F. Fredricks, and B.A.S. Van Mooy. 2016. LOBSTAHS: An adduct-based lipidomics strategy for discovery and identification of oxidative stress biomarkers. Analytical Chemistry 88:7154-7162

See Also

generateLOBdbase, loadLOBdbase, doLOBscreen, LOBdbase

Examples

## return object information

showClass("LOBdbase")

hholm/LOBSTAHS documentation built on March 17, 2024, 1:53 a.m.