loadLOBdbase {LOBSTAHS} | R Documentation

## 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, james.r.collins@aya.yale.edu

### 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)

[Package LOBSTAHS version 1.14.0 Index]