LOBSet-class: Class LOBSet: Peak data with annotations, isomers, and...

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

Class LOBSet: Peak data with annotations, isomers, and compound assignments

Description

A class for HPLC-MS peak data that have been screened and annotated using LOBSTAHS function doLOBscreen.

Objects from the class

Objects can be created with the LOBSet constructor. A 'LOBSet' can also be created by calls of the form new("LOBSet", ...).

Slots

peakdata:

Object of class "data.frame", containing peakdata by compound assignment

iso_C3r:

Object of class "list", a list of the match_IDs of possible regioisomers of each compound

iso_C3f:

Object of class "list", a list of the match_IDs of possible functional structural isomers of each compound

iso_C3c:

Object of class "list", a list of the match_IDs of possible isobars of this compound

LOBscreen_diagnostics:

Object of class "data.frame", numbers of peaks, peakgroups, adducts, and unique parent compounds present in the dataset after application of each screening criterion in doLOBscreen

LOBisoID_diagnostics:

Object of class "data.frame", numbers of peakgroups and parent compounds to which the various isomer annotations have been assigned

LOBscreen_settings:

Object of class "list", captures the settings used in doLOBscreen to generate the "LOBSet"

polarity:

Object of class "factor", polarity of data in the "LOBSet"

sampnames:

Object of class "character", the names of the samples from which the "LOBSet" was generated

Methods

show

signature(object = "LOBSet"): ...

LOBisoID_diagnostics

signature(object = "LOBSet"): get LOBisoID_diagnostics slot

LOBscreen_diagnostics

signature(object = "LOBSet"): get LOBscreen_diagnostics slot

LOBscreen_settings

signature(object = "LOBSet"): get LOBscreen_settings slot

sampnames

signature(object = "LOBSet"): get sampnames slot

peakdata

signature(object = "LOBSet"): get peakdata slot

polarity

signature(object = "LOBSet"): get polarity slot

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

doLOBscreen, getLOBpeaklist, LOBSet, xsAnnotate

Examples

## return object information

showClass("LOBSet")

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