getLOBpeaklist {LOBSTAHS} | R Documentation

## Export screened LOBSTAHS peaklist with compound assignments

### Description

Extracts screened peak data, compound assignments, annotation codes, and (optionally) isomer data from a `LOBSet-class` object. Returns a table containing the requested data, with option to export to a .csv file.

### Usage

    getLOBpeaklist(LOBSet, include.iso = TRUE, include.unidentified = TRUE,
                   gen.csv = FALSE)

### Arguments

`LOBSet` | A LOBSTAHS `"LOBSet"` object.
`include.iso` | Specify whether isomer and isobar identification data should be included in peaklist.
`include.unidentified` | If data for unidentified or discarded features is present in the `LOBSet`, should these data be exported with the peaklist? A value of `FALSE` will yield a peaklist that includes data only for those features to which one or more LOBSTAHS compound identities have been assigned.
`gen.csv` | Should a .csv file be generated in addition to the data frame that is returned?

### Details

`getLOBpeaklist` extracts data from all slots in a given `"LOBSet"` object and flows it into a data frame. Annotation codes indicating compliance with the adduct ion hierarchy screening criteria are appended to the m/z, retention time, and peak area data for each xcms peakgroup remaining in the final dataset.

If `include.iso = TRUE`, three additional columns containing the `match_IDs` of the possible isomers and isobars for each peakgroup are also appended. `getLOBpeaklist` does not export any of the diagnostic data in the `LOBSet` `LOBscreen_diagnostics` or `LOBisoID_diagnostics` slots.

When the `LOBSet` includes peak data for features that were not identified during screening or were discarded (i.e., if the user specified `retain.unidentified = TRUE` when calling `doLOBscreen`), the user is given the option to export these data when using `getLOBpeaklist`. This is useful when untargeted follow-on data analysis is anticipated, or the user simply wants to export data for all features present in the original dataset, not just those for which a LOBSTAHS identity was found.

### Value

A data frame with the following structure:

`match_ID`:

  Object of class `"integer"`, unique identifier for each assignment of a compound to a peakgroup (multiple `match_ID`s can exist for a peakgroup if the group was assigned multiple compound identities

`compound_name`:

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

`elem_formula`:

  Object of class `"character"`, empirical formula of compound

`LOBdbase_mz`:

  Object of class `"numeric"`, calculated m/z of the adduct for which data in this group are reported; obtained database

`peakgroup_mz`:

  Object of class `"numeric"`, mean observed m/z of the feature in this peakgroup across all samples in which it was identified

`LOBdbase_ppm_match`:

  Object of class `"numeric"`, ppm deviation between observed and calculated m/z

`peakgroup_rt`:

  Object of class `"numeric"`, mean observed retention time of the feature in this peakgroup across all samples in which it was identified

`peakgroup_mzmin`:

  Object of class `"numeric"`, minimum observed m/z of feature across samples

`peakgroup_mzmax`:

  Object of class `"numeric"`, maximum observed m/z of feature across samples

`peakgroup_rtmin`:

  Object of class `"numeric"`, minimum observed retention time of feature across samples

`peakgroup_rtmax`:

  Object of class `"numeric"`, maximum observed retention time of feature across samples

peak area data:

  Several objects of class `"numeric"`, containing integrated peak area data for this group by sample (one column for each sample in the dataset)

`xcms_peakgroup`:

  Object of class `"integer"`, the xcms `xcmsSet` peakgroup identifier

`CAMERA_pseudospectrum`:

  Object of class `"integer"`, the CAMERA `xsAnnotate` pseudospectrum identifier

`LOBdbase_frag_ID`:

  Object of class `"integer"`, the `LOBdbase` fragment ID corresponding to the adduct of this compound for which data are reported; this is the dominant adduct of the compound according to the adduct ion hierarchy rules for the parent lipid class

`LOBdbase_exact_parent_neutral_mass`:

  Object of class `"numeric"`, the calculated exact (monoisotopic) mass of the compound; from database

`lipid_class`:

  Object of class `"factor"`, parent lipid class of this compound

`species`:

  Object of class `"character"`, if a pigment or IP-DAG, the specific compound species

`major_adduct`:

  Object of class `"factor"`, adduct of the compound for which data in this entry is reported

`FA_total_no_C`:

  Object of class `"integer"`, total number of acyl (fatty acid) carbon atoms in this 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 this 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 on this compound, compared with its unoxidized parent

`C1`-`C6b`:

  Several objects of class `"integer"`, containing binary indicators for each possible annotation code applied by `doLOBscreen`

`casecodes`:

  Object of class `"character"`, character string containing list of all codes applied to this assignment

`iso_C3r_match_ID`:

  Object of class `"character"`, character string of integer containing the `match_ID`s of all possible regioisomers of this compound (if `include.iso = TRUE`)

`iso_C3f_match_ID`:

  Object of class `"character"`, character string of integer containing the `match_ID`s of all possible functional structural isomers of this compound (if `include.iso = TRUE`)

`iso_C3c_match_ID`:

  Object of class `"character"`, character string of integer containing the `match_ID`s of all possible isobars of this compound (if `include.iso = TRUE`)

### 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

`LOBSet`, `LOBSet`, `doLOBscreen`

### Examples

    ## export peaklist, with isomer data, but without data for unidentified features
    library(PtH2O2lipids)

    PtH2O2.peakdata = getLOBpeaklist(ptH2O2lipids$LOBSet, include.iso = TRUE,
                                     include.unidentified = FALSE, gen.csv = FALSE)

[Package LOBSTAHS version 1.14.0 Index]