loadLOBdbase: Import and reconstruct LOBdbase from a text file

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

Import and reconstruct LOBdbase from a text file

Description

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

Usage

loadLOBdbase(file, polarity, num_compounds = NULL)

Arguments

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.

Details

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.

Value

A "LOBdbase-class" object.

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

LOBdbase, LOBdbase, doLOBscreen, generateLOBdbase, default.LOBdbase

Examples

## 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)

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