LOBdbase-class {LOBSTAHS} | R Documentation

## Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases

### Description

A class for `LOBSTAHS` databases that contain a combination of in silico and empirical data for a wide range of lipids, oxidized lipids, and oxylipins.

### Objects from the class

Objects can be created using the simulation function `generateLOBdbase` (preferred; satisfies the needs of most users), imported from a .csv file of proper format using `loadLOBdbase`, or created using the rudimentary constructor `LOBdbase` (least preferred). A 'LOBdbase' can also be created by calls of the form `new("LOBdbase", ...)`.

### Slots

`frag_ID`:

  Object of class `"integer"`, a unique identifier for this molecular species

`mz`:

  Object of class `"numeric"`, the calculated m/z of this species

`exact_parent_neutral_mass`:

  Object of class `"numeric"`, the calculated (monoisotopic) exact mass of the parent compound of this species

`lipid_class`:

  Object of class `"factor"`, the parent lipid class of this species

`species`:

  Object of class `"character"`, the lipid subclass

`adduct`:

  Object of class `"factor"`, the adduct ion represented by this entry

`adduct_rank`:

  Object of class `"integer"`, the relative abundance ranking of this adduct relative to the other adducts of the same parent compound

`FA_total_no_C`:

  Object of class `"integer"`, total number of acyl (fatty acid) carbon atoms in the parent compound; `NA` if `lipid_class` is not TAG, IP-DAG, PUA, or FFA

`FA_total_no_DB`:

  Object of class `"integer"`, total number of acyl (fatty acid) carbon-carbon double bonds in the parent compound; `NA` if `lipid_class` is not TAG, IP-DAG, PUA, or FFA

`degree_oxidation`:

  Object of class `"integer"`, number of additional oxygen atoms present

`parent_elem_formula`:

  Object of class `"character"`, elemental formula of the parent compound

`parent_compound_name`:

  Object of class `"character"`, name of the parent compound; see the reference for this entry for the naming convention applied to compounds other than pigments

`polarity`:

  Object of class `"factor"`, ionization mode of data in the database

`num_entries`:

  Object of class `"integer"`, number of total entries (adducts) in the database

`num_compounds`:

  Object of class `"integer"`, number of parent compounds represented in the database (should be < `num_entries`)

### Methods

show

  `signature(object = "LOBdbase")`: ...

polarity

  `signature(object = "LOBdbase")`: get `polarity` slot

num_compounds

  `signature(object = "LOBdbase")`: get `num_compounds` slot

num_entries

  `signature(object = "LOBdbase")`: get `num_entries` slot

frag_ID

  `signature(object = "LOBdbase")`: get `frag_ID` slot

exact_parent_neutral_mass

  `signature(object = "LOBdbase")`: get `exact_parent_neutral_mass` slot

lipid_class

  `signature(object = "LOBdbase")`: get `lipid_class` slot

species

  `signature(object = "LOBdbase")`: get `species` slot

adduct

  `signature(object = "LOBdbase")`: get `adduct` slot

adduct_rank

  `signature(object = "LOBdbase")`: get `adduct_rank` slot

FA_total_no_C

  `signature(object = "LOBdbase")`: get `FA_total_no_C` slot

FA_total_no_DB

  `signature(object = "LOBdbase")`: get `FA_total_no_DB` slot

degree_oxidation

  `signature(object = "LOBdbase")`: get `degree_oxidation` slot

parent_elem_formula

  `signature(object = "LOBdbase")`: get `parent_elem_formula` slot

parent_compound_name

  `signature(object = "LOBdbase")`: get `parent_compound_name` slot

### 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

`generateLOBdbase`, `loadLOBdbase`, `doLOBscreen`, `LOBdbase`

### Examples

    ## return object information

    showClass("LOBdbase")

[Package LOBSTAHS version 1.12.0 Index]