loadLOBdbase: Import and reconstruct LOBdbase from a text file
In LOBSTAHS: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

Description Usage Arguments Details Value Author(s) References See Also Examples

Reconstruct a "LOBdbase" object from properly formatted data in a .csv file. More robust than the generic constructor function LOBdbase.

1	loadLOBdbase(file, polarity, num_compounds = NULL)

`file`	Path to a .csv file containing the database to be imported. The file format should be consistent with the .csv output that is obtained using `gen.csv = TRUE` in `generateLOBdbase`. Some leeway is allowed for variation in capitalization and punctuation of column headers.
`polarity`	Specify polarity (ionization mode) of the database being imported ("positive" or "negative"). `loadLOBdbase` will attempt to detect the polarity mode based on data in the "adduct" column if nothing is given.
`num_compounds`	If known, the number of parent compounds represented in the database being imported. Can be unspecified.

loadLOBdbase is a glorified implementation of read.table that attempts to determine whether the format of the data in file is consistent with that of a saved "LOBdbase" object. Some leeway is allowed for variation in punctuation and spelling of column headers in the source file. Special attention should be paid to how adduct ions are specified (e.g., "[M+H]+", "[M+NH4]+", or "[M+Cl]-"). Most users will find this function more useful than the generic constructor function LOBdbase.

A "LOBdbase-class" object.

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

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

LOBdbase, LOBdbase, doLOBscreen, generateLOBdbase, default.LOBdbase

## save the default negative mode database as a .csv file

data(default.LOBdbase)

neg.DB = default.LOBdbase$negative

fname = paste0("LOBSTAHS_lipid-oxy_DB_",
               strtrim(as.character(polarity(neg.DB)),3),".csv")

exportmat = data.frame(frag_ID(neg.DB),
                         mz(neg.DB),
                         exact_parent_neutral_mass(neg.DB),
                         as.character(lipid_class(neg.DB)),
                         as.character(species(neg.DB)),
                         as.character(adduct(neg.DB)),
                         as.character(adduct_rank(neg.DB)),
                         FA_total_no_C(neg.DB),
                         FA_total_no_DB(neg.DB),
                         degree_oxidation(neg.DB),
                         parent_elem_formula(neg.DB),
                         parent_compound_name(neg.DB),
                         stringsAsFactors = FALSE)

colnames(exportmat) = c("frag_ID","mz","exact_parent_neutral_mass",
                        "lipid_class","species","adduct","adduct_rank",
                        "FA_total_no_C","FA_total_no_DB","degree_oxidation",
                        "parent_elem_formula","parent_compound_name")

write.csv(exportmat, fname)

## reimport it

neg.DB.reimported = loadLOBdbase("LOBSTAHS_lipid-oxy_DB_neg.csv",
                                 polarity = "negative",
                                 num_compounds = NULL)