getLOBpeaklist: Export screened LOBSTAHS peaklist with compound assignments

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

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_IDs 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_IDs 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_IDs 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_IDs of all possible isobars of this compound (if include.iso = TRUE)

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

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)

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