LOBdbase | R Documentation |
Constructor function for manual assembly or reconstruction of a
LOBdbase
object to be used in screening data with the
LOBSTAHS
function doLOBscreen
.
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)
frag_ID |
An object of class |
mz |
An object of class |
exact_parent_neutral_mass |
An object of class |
lipid_class |
An object of class |
species |
An object of class |
adduct |
An object of class |
adduct_rank |
An object of class |
FA_total_no_C |
An object of class |
FA_total_no_DB |
An object of class |
degree_oxidation |
An object of class |
parent_elem_formula |
An object of class |
parent_compound_name |
An object of class |
polarity |
An object of class |
num_entries |
An object of class |
num_compounds |
An object of class |
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.
A "LOBdbase-class"
object.
James Collins, james.r.collins@aya.yale.edu
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.
generateLOBdbase
,
loadLOBdbase
,
doLOBscreen
,
LOBdbase
## 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)
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