R: LOBSet constructor for manual creation or reconstruction of a...

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

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 1.14.0 Index]