LOBdbase: LOBdbase constructor for manual creation or reconstruction of...

View source: R/LOBdbase.R

LOBdbaseR 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.

See Also

generateLOBdbase, loadLOBdbase, doLOBscreen, LOBdbase

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.