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 1.14.0
Index]