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

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

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_IDs 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_IDs 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_IDs 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, [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, 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)

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