LOBSet {LOBSTAHS} | R Documentation

## LOBSet constructor for manual creation or reconstruction of a LOBSet object

### Description

Constructor function for manual creation or reconstruction of a `LOBSet` object for HPLC-MS peak data that have been screened using `LOBSTAHS`.

### Usage

    LOBSet(peakdata = NULL, iso_C3r = NULL, iso_C3f = NULL, iso_C3c = NULL,
           LOBscreen_diagnostics = NULL, LOBisoID_diagnostics = NULL,
           LOBscreen_settings = NULL, polarity = c("positive","negative"),
           sampnames = NULL)

### Arguments

`peakdata` | An object of class `"data.frame"` containing peak data and LOBSTAHS annotation information by assignment. Column headings and data types should conform to those of the peakdata slot of a `LOBSet-class` object produced using the function `doLOBscreen`. Each row in the peakdata table represents one compound assignment made by LOBSTAHS. The format of the data frame occupying the peakdata slot in a `LOBSet` object can be obtained using the `peakdata` accessor for objects of `LOBSet-class`.
`iso_C3r` | An object of class `"list"`, a list of the `match_ID`s of possible regioisomers of each compound for which there is a row in `peakdata`. Length of `iso_C3r` should equal the number of rows in the data frame given for `peakdata`.
`iso_C3f` | An object of class `"list"`, a list of the `match_ID`s of possible functional structural isomers of each compound for which there is a row in `peakdata`. Length of `iso_C3f` should equal the number of rows in the data frame given for `peakdata`.
`iso_C3c` | An object of class `"list"`, a list of the `match_ID`s of the isobars of each compound for which there is a row in `peakdata`. Length of `iso_C3c` should equal the number of rows in the data frame given for `peakdata`.
`LOBscreen_diagnostics` | An object of class `"data.frame"`, containing diagnostic information recorded by the function `doLOBscreen` during creation of a `LOBSet`. The numbers of peaks, peakgroups, adducts, and unique parent compounds present the dataset after application of each LOBSTAHS screening criterion.
`LOBisoID_diagnostics` | An object of class `"data.frame"`, containing isomer and isobar summary statistics. The numbers of peakgroups and parent compounds to which the various isomer identifications have been applied by `doLOBscreen` to a given `LOBSet`.
`LOBscreen_settings` | An object of class `"list"`; the settings used in `doLOBscreen` to generate the `LOBSet`
`polarity` | An object of class `"factor"`, polarity of data in the `LOBSet`. Must be either "negative" or "positive."
`sampnames` | An object of class `"character"`; the names of the samples from which the `LOBSet` was generated.

### Details

Typically, a `LOBSet` will be created from a CAMERA `xsAnnotate-class` object using the `LOBSTAHS` function `doLOBscreen`. The `LOBSet` constructor function is therefore provided only for manual object creation; it will not be needed by most users.

### Value

A `"LOBSet-class"` object.

### 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`, `doLOBscreen`, `xsAnnotate`

### Examples

    ## create an empty LOBSet for positive ion mode data

    myLOBSet = LOBSet(peakdata = NULL, iso_C3r = NULL, iso_C3f = NULL,
                      iso_C3c = NULL, LOBscreen_diagnostics = NULL,
                      LOBisoID_diagnostics = NULL, LOBscreen_settings = NULL,
                      polarity = "positive", sampnames = NULL)

[Package LOBSTAHS version 1.13.0 Index]