LOBdbase: LOBdbase constructor for manual creation or reconstruction of...
In hholm/LOBSTAHS: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

LOBdbase

R Documentation

LOBdbase constructor for manual creation or reconstruction of a LOBdbase object

Description

Constructor function for manual assembly or reconstruction of a LOBdbase object to be used in screening data with the LOBSTAHS function doLOBscreen.

Usage

LOBdbase(frag_ID = NULL, mz = NULL, exact_parent_neutral_mass = NULL,
        lipid_class = NULL, species = NULL, adduct = NULL, adduct_rank = NULL,
        FA_total_no_C = NULL, FA_total_no_DB = NULL, degree_oxidation = NULL,
        parent_elem_formula = NULL, parent_compound_name = NULL,
        polarity = NULL, num_entries = NULL, num_compounds = NULL)

Arguments

`frag_ID`	An object of class `"integer"`; vector of unique identifiers for the molecular species in the database.
`mz`	An object of class `"numeric"`; calculated m/z of each species for which an entry exists.
`exact_parent_neutral_mass`	An object of class `"numeric"`; calculated (monoisotopic) exact masses of the parent compound of each species.
`lipid_class`	An object of class `"factor"`; parent lipid classes of each species
`species`	An object of class `"character"`; the lipid subclasses of each species
`adduct`	An object of class `"factor"`; the adduct ions represented by each entry
`adduct_rank`	An object of class `"integer"`; the relative abundance rankings of each adduct relative to the other adducts of the same parent compound
`FA_total_no_C`	An object of class `"integer"`; the total number of acyl (fatty acid) carbon atoms in the parent compound of each entry; values should be `NA` where `lipid_class` is not TAG, IP-DAG, PUA, or FFA
`FA_total_no_DB`	An object of class `"integer"`; the total number of acyl (fatty acid) carbon-carbon double bonds in the parent compound of each entry; values should be `NA` where `lipid_class` is not TAG, IP-DAG, PUA, or FFA
`degree_oxidation`	An object of class `"integer"`; the number of additional oxygen atoms present on each species
`parent_elem_formula`	An object of class `"character"`; the elemental formulae of the parent compound of each species
`parent_compound_name`	An object of class `"character"`; names of the parent compound of each species; see the reference for this entry for snaming conventions that should be applied for pigments and compounds other than pigments
`polarity`	An object of class `"factor"` with length = 1; the ionization mode of data in the database to be constructed
`num_entries`	An object of class `"integer"` with length = 1; the number of total entries (adducts) in the database to be constructed. If specified, the value of `num_entries` should be equal to the length of any arguments that contain database data
`num_compounds`	An object of class `"integer"` with length = 1; the number of parent compounds represented in the database to be constructed. If specified, the value of `num_compounds` should be < the value specifed for `num_entries`.

Details

Typically, a LOBdbase will be created using the in silico simulation function generateLOBdbase. Formatted database entries (such as from an external .csv file) can be loaded using loadLOBdbase. The rudimentary LOBdbase constructor function is therefore provided only for manual object creation; it will not be needed by most users. All arguments except for those containing metadata (i.e., polarity, num_entries, and num_compounds) should be of the same length.

Value

A "LOBdbase-class" object.

Author(s)

James Collins, james.r.collins@aya.yale.edu

References

The LOBSTAHS package is presented in:

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, doi:10.1021/acs.analchem.6b01260.

Data for lipid classes BLL, PDPT, vGSL, sGSL, hGSL, hapGSL, and hapCER are as described in:

Hunter J. E., M. J. Frada, H. F. Fredricks, A. Vardi, and B. A. S. Van Mooy. 2015. Targeted and untargeted lipidomics of Emiliania huxleyi viral infection and life cycle phases highlights molecular biomarkers of infection, susceptibility, and ploidy. Frontiers in Marine Science 2:81, doi:10.3389/fmars.2015.00081

Fulton, J. M., H. F. Fredricks, K. D. Bidle, A. Vardi, B. J. Kendrick, G. R. DiTullio, and B. A. S. Van Mooy. 2014. Novel molecular determinants of viral susceptibility and resistance in the lipidome of Emiliania huxleyi, Environmental Microbiology 16(4):1137-1149, doi:10.1111/1462-2920.12358.

Examples

## create an empty LOBdbase

myLOBdbase = LOBdbase(frag_ID = NULL, mz = NULL,
                      exact_parent_neutral_mass = NULL, lipid_class = NULL,
                      species = NULL, adduct = NULL, adduct_rank = NULL,
                      FA_total_no_C = NULL, FA_total_no_DB = NULL,
                      degree_oxidation = NULL, parent_elem_formula = NULL,
                      parent_compound_name = NULL, polarity = NULL,
                      num_entries = NULL, num_compounds = NULL)

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