## ----eval = FALSE-------------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly=TRUE))
# install.packages("BiocManager")
# BiocManager::install("xcms")
# BiocManager::install("CAMERA")
## ----eval = FALSE-------------------------------------------------------------
# install.packages("devtools")
## ----eval = FALSE-------------------------------------------------------------
# library("devtools")
# install_github("vanmooylipidomics/LOBSTAHS", build_vignettes = TRUE)
## ----eval = FALSE-------------------------------------------------------------
# ## install dataset 'PtH2O2lipids'
# ## see LOBSTAHS documentation for examples
#
# install_github("vanmooylipidomics/PtH2O2lipids")
## ----eval = FALSE-------------------------------------------------------------
# system(paste("msconvert Exactive_data.raw --mzXML --filter \"peakPicking true 1-\" -o mzXML_ms1_two_mode -v"))
## ----eval = FALSE-------------------------------------------------------------
# system(paste("msconvert mzXML_ms1_two_mode/Exactive_data.mzXML --mzXML --filter \"polarity positive\" -o mzXML_ms1_pos_mode -v"))
# system(paste("msconvert mzXML_ms1_two_mode/Exactive_data.mzXML --mzXML --filter \"polarity negative\" -o mzXML_ms1_neg_mode -v"))
## ----warning = FALSE, message = FALSE, eval = FALSE---------------------------
# library(xcms)
# library(CAMERA)
# library(LOBSTAHS)
#
# # first, a necessary workaround to avoid a import error; see
# # https://support.bioconductor.org/p/69414/
#
# imports = parent.env(getNamespace("CAMERA"))
# unlockBinding("groups", imports)
# imports[["groups"]] = xcms::groups
# lockBinding("groups", imports)
#
# # create annotated xset using wrapper annotate(), allowing us to perform all
# # CAMERA tasks at once
#
# xsA = annotate(ptH2O2lipids$xsAnnotate@xcmsSet,
#
# quick=FALSE,
# sample=NA, # use all samples
# nSlaves=1, # set to number of available cores or processors if
# # > 1
#
# # group FWHM settings (defaults)
#
# sigma=6,
# perfwhm=0.6,
#
# # groupCorr settings (defaults)
#
# cor_eic_th=0.75,
# graphMethod="hcs",
# pval=0.05,
# calcCiS=TRUE,
# calcIso=TRUE,
# calcCaS=FALSE,
#
# # findIsotopes settings
#
# maxcharge=4,
# maxiso=4,
# minfrac=0.5,
#
# # adduct annotation settings
#
# psg_list=NULL,
# rules=NULL,
# polarity="positive", # the PtH2O2lipids xcmsSet contains
# # positive-mode data
# multiplier=3,
# max_peaks=100,
#
# # common to multiple tasks
#
# intval="into",
# ppm=2.5,
# mzabs=0.0015
#
# )
# #> Start grouping after retention time.
# #> Created 113 pseudospectra.
# #> Generating peak matrix!
# #> Run isotope peak annotation
# #> % finished: 10 20 30 40 50 60 70 80 90 100
# #> Found isotopes: 5692
# #> Start grouping after correlation.
# #> Generating EIC's ..
# #>
# #> Calculating peak correlations in 113 Groups...
# #> % finished: 10 20 30 40 50 60 70 80 90 100
# #>
# #> Calculating isotope assignments in 113 Groups...
# #> % finished: 10 20 30 40 50 60 70 80 90 100
# #> Calculating graph cross linking in 113 Groups...
# #> % finished: 10 20 30 40 50 60 70 80 90 100
# #> New number of ps-groups: 5080
# #> xsAnnotate has now 5080 groups, instead of 113
# #> Generating peak matrix for peak annotation!
# #>
# #> Calculating possible adducts in 5080 Groups...
# #> % finished: 10 20 30 40 50 60 70 80 90 100
## ----warning = FALSE, message = FALSE-----------------------------------------
library(LOBSTAHS)
data(default.LOBdbase)
default.LOBdbase$positive # default positive mode database
default.LOBdbase$negative # default negative mode database
## ----warning = FALSE, message = FALSE, eval = FALSE---------------------------
# data(default.acylRanges)
# data(default.oxyRanges)
# data(default.componentCompTable)
# data(default.adductHierarchies)
## ----eval = FALSE-------------------------------------------------------------
# LOBdb = generateLOBdbase(polarity = c("positive","negative"), gen.csv = FALSE,
# component.defs = NULL, AIH.defs = NULL, acyl.ranges = NULL,
# oxy.ranges = NULL)
#
## ----eval = FALSE-------------------------------------------------------------
# data(default.rt.windows)
## ----eval = FALSE-------------------------------------------------------------
# myPtH2O2LOBSet = doLOBscreen(ptH2O2lipids$xsAnnotate, polarity = "positive",
# database = NULL, remove.iso = TRUE,
# rt.restrict = TRUE, rt.windows = NULL,
# exclude.oddFA = TRUE, match.ppm = 2.5,
# retain.unidentified = FALSE)
## ----warning = FALSE, message = FALSE, eval = FALSE---------------------------
# ptH2O2lipids$LOBSet
# #> A positive polarity "LOBSet" containing LC-MS peak data. Compound assignments
# #> and adduct ion hierarchy screening annotations applied to 16 samples using the
# #> "LOBSTAHS" package.
# #>
# #> No. individual peaks with LOBSTAHS compound assignments: 21869
# #> No. peak groups with LOBSTAHS compound assignments: 1595
# #> No. LOBSTAHS compound assignments: 1969
# #> m/z range of features identified using LOBSTAHS: 551.425088845409-1269.09515435315
# #>
# #> Identified peak groups having possible regisomers: 556
# #> Identified peak groups having possible structural functional isomers: 375
# #> Identified peak groups having isobars indistinguishable within ppm matching
# #> tolerance: 84
# #>
# #> Restrictions applied prior to conducting adduct ion hierarchy screening:
# #> remove.iso, rt.restrict, exclude.oddFA
# #>
# #> Match tolerance used for LOBSTAHS database assignments: 2.5 ppm
# #>
# #> Memory usage: 1.26 MB
## ----warning = FALSE, message = FALSE, eval = FALSE---------------------------
# LOBscreen_diagnostics(ptH2O2lipids$LOBSet)
# #> peakgroups peaks assignments parent_compounds
# #> initial 18314 251545 NA NA
# #> post_remove_iso 12146 163938 NA NA
# #> initial_assignments 5077 67862 15929 14076
# #> post_rt_restrict 4451 60070 13504 11779
# #> post_exclude_oddFA 3871 52337 7458 6283
# #> post_AIHscreen 1595 21869 2056 1969
## ----warning = FALSE, message = FALSE, eval = FALSE---------------------------
# LOBisoID_diagnostics(ptH2O2lipids$LOBSet)
# #> peakgroups parent_compounds assignments features
# #> C3r_regio.iso 556 352 750 7591
# #> C3f_funct.struct.iso 375 577 752 5057
# #> C3c_isobars 84 162 195 1137