LOBSet-class {LOBSTAHS} | R Documentation

## 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_ID`s of possible regioisomers of each compound

`iso_C3f`:

  Object of class `"list"`, a list of the `match_ID`s of possible functional structural isomers of each compound

`iso_C3c`:

  Object of class `"list"`, a list of the `match_ID`s 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, 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

`doLOBscreen`, `getLOBpeaklist`, `LOBSet`, `xsAnnotate`

### Examples

    ## return object information

    showClass("LOBSet")

[Package LOBSTAHS version 1.14.0 Index]