## ---- 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