LOBSTAHS: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Version 1.2.0

LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.

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AuthorJames Collins [aut, cre], Helen Fredricks [aut], Bethanie Edwards [aut], Benjamin Van Mooy [aut]
Bioconductor views DataImport Lipidomics MassSpectrometry Metabolomics
Date of publicationNone
MaintainerJames Collins <james.r.collins@aya.yale.edu>
LicenseGPL (>= 3) + file LICENSE
Version1.2.0
URL http://bioconductor.org/packages/LOBSTAHS
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("LOBSTAHS")

Man pages

doLOBscreen: Screen, annotate, and identify compounds in an xsAnnotate...
exportDBtoCSV: Export a LOBSTAHS database (LOBdbase) object to a text file
extractLOBdbasedata: Extract compound data from a LOBdbase
generateLOBdbase: Conduct _in silico_ simulation and generate lipid-oxylipin...
getLOBpeaklist: Export screened LOBSTAHS peaklist with compound assignments
loadLOBdbase: Import and reconstruct LOBdbase from a text file
LOBdbase: LOBdbase constructor for manual creation or reconstruction of...
LOBdbase-class: Class LOBdbase: A class for LOBSTAHS lipid-oxylipin databases
LOBdefaults: LOBSTAHS default databases and database generation parameters
LOBSet: LOBSet constructor for manual creation or reconstruction of a...
LOBSet-class: Class LOBSet: Peak data with annotations, isomers, and...

Functions

FA_total_no_C Man page
FA_total_no_C,LOBdbase-method Man page
FA_total_no_C<- Man page
FA_total_no_C<-,LOBdbase-method Man page
FA_total_no_DB Man page
FA_total_no_DB,LOBdbase-method Man page
FA_total_no_DB<- Man page
FA_total_no_DB<-,LOBdbase-method Man page
LOBSet Man page Source code
LOBSet-class Man page
LOBdbase Man page Source code
LOBdbase-class Man page
LOBdefaults Man page
LOBisoID_diagnostics Man page
LOBisoID_diagnostics,LOBSet-method Man page
LOBisoID_diagnostics<- Man page
LOBisoID_diagnostics<-,LOBSet-method Man page
LOBscreen_diagnostics Man page
LOBscreen_diagnostics,LOBSet-method Man page
LOBscreen_diagnostics<- Man page
LOBscreen_diagnostics<-,LOBSet-method Man page
LOBscreen_settings Man page
LOBscreen_settings,LOBSet-method Man page
LOBscreen_settings<- Man page
LOBscreen_settings<-,LOBSet-method Man page
adduct Man page
adduct,LOBdbase-method Man page
adduct<- Man page
adduct<-,LOBdbase-method Man page
adduct_rank Man page
adduct_rank,LOBdbase-method Man page
adduct_rank<- Man page
adduct_rank<-,LOBdbase-method Man page
calcComponentMasses Source code
calcNumCombs Source code
combCalc Source code
default.LOBdbase Man page
default.acylRanges Man page
default.adductHierarchies Man page
default.componentCompTable Man page
default.oxyRanges Man page
default.rt.windows Man page
defineElemExactMasses Source code
degree_oxidation Man page
degree_oxidation,LOBdbase-method Man page
degree_oxidation<- Man page
degree_oxidation<-,LOBdbase-method Man page
doLOBscreen Man page Source code
evalFeatureRT Source code
exact_parent_neutral_mass Man page
exact_parent_neutral_mass,LOBdbase-method Man page
exact_parent_neutral_mass<- Man page
exact_parent_neutral_mass<-,LOBdbase-method Man page
excludeoddFAlength Source code
exportDBtoCSV Man page Source code
extractLOBdbasedata Man page Source code
frag_ID Man page
frag_ID,LOBdbase-method Man page
frag_ID<- Man page
frag_ID<-,LOBdbase-method Man page
genTimeStamp Source code
generateLOBdbase Man page Source code
getLOBpeaklist Man page Source code
getformattedIsoData Source code
lipid_class Man page
lipid_class,LOBdbase-method Man page
lipid_class<- Man page
lipid_class<-,LOBdbase-method Man page
loadAIH Source code
loadLOBdbase Man page Source code
loadSimRanges Source code
matchbyPPM Source code
mz Man page
mz,LOBdbase-method Man page
mz<- Man page
mz<-,LOBdbase-method Man page
num_compounds Man page
num_compounds,LOBdbase-method Man page
num_compounds<- Man page
num_compounds<-,LOBdbase-method Man page
num_entries Man page
num_entries,LOBdbase-method Man page
num_entries<- Man page
num_entries<-,LOBdbase-method Man page
parent_compound_name Man page
parent_compound_name,LOBdbase-method Man page
parent_compound_name<- Man page
parent_compound_name<-,LOBdbase-method Man page
parent_elem_formula Man page
parent_elem_formula,LOBdbase-method Man page
parent_elem_formula<- Man page
parent_elem_formula<-,LOBdbase-method Man page
peakdata Man page
peakdata,LOBSet-method Man page
peakdata<- Man page
peakdata<-,LOBSet-method Man page
polarity Man page
polarity,LOBSet-method Man page
polarity,LOBdbase-method Man page
polarity<- Man page
polarity<-,LOBSet-method Man page
polarity<-,LOBdbase-method Man page
runSim Source code
sampnames Man page
sampnames,LOBSet-method Man page
sampnames<- Man page
sampnames<-,LOBSet-method Man page
screenPSpectrum Source code
show,LOBSet-method Man page
show,LOBdbase-method Man page
species Man page
species,LOBdbase-method Man page
species<- Man page
species<-,LOBdbase-method Man page
trimAssignments Source code

Files

.BBSoptions
DESCRIPTION
LICENSE
NAMESPACE
R
R/LOBSet.R
R/LOBdbase.R
R/doLOBscreen.R
R/generateLOBdbase.R
README.md
build
build/vignette.rds
data
data/datalist
data/default.LOBdbase.RData
data/default.acylRanges.RData
data/default.adductHierarchies.RData
data/default.componentCompTable.RData
data/default.oxyRanges.RData
data/default.rt.windows.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/LOBSTAHS.R
inst/doc/LOBSTAHS.Rmd
inst/doc/LOBSTAHS.html
inst/doc/csv
inst/doc/csv/LOBSTAHS_acylRanges.csv
inst/doc/csv/LOBSTAHS_adductHierarchies.csv
inst/doc/csv/LOBSTAHS_componentCompTable.csv
inst/doc/csv/LOBSTAHS_oxyRanges.csv
inst/doc/csv/LOBSTAHS_rt.windows.csv
inst/doc/xlsx
inst/doc/xlsx/LOBSTAHS_acylRanges.xlsx
inst/doc/xlsx/LOBSTAHS_adductHierarchies.xlsx
inst/doc/xlsx/LOBSTAHS_componentCompTable.xlsx
inst/doc/xlsx/LOBSTAHS_oxyRanges.xlsx
inst/doc/xlsx/LOBSTAHS_rt.windows.xlsx
man
man/LOBSet-class.Rd
man/LOBSet.Rd
man/LOBdbase-class.Rd
man/LOBdbase.Rd
man/LOBdefaults.Rd
man/doLOBscreen.Rd
man/exportDBtoCSV.Rd
man/extractLOBdbasedata.Rd
man/generateLOBdbase.Rd
man/getLOBpeaklist.Rd
man/loadLOBdbase.Rd
vignettes
vignettes/LOBSTAHS.Rmd
vignettes/images
vignettes/images/Fig1.jpg
vignettes/images/Fig2.png
vignettes/images/Fig3.png
vignettes/images/Fig4.png
vignettes/images/Fig5.png
vignettes/images/Flow_thumb.png
LOBSTAHS documentation built on May 20, 2017, 11:02 p.m.