## ---- eval = FALSE-------------------------------------------------------
## source("http://bioconductor.org/biocLite.R")
## biocLite("CAMERA")
## biocLite("xcms")

## ---- eval = FALSE-------------------------------------------------------
## install.packages("devtools")

## ---- eval = FALSE-------------------------------------------------------
## library("devtools")
## install_github("vanmooylipidomics/LOBSTAHS")

## ---- 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-----------------------------------
library(PtH2O2lipids)
ptH2O2lipids$xsAnnotate@xcmsSet

## ---- 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)

## ---- 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.
## #>
## #> Individual peaks: 21869
## #> Peak groups: 1595
## #> Compound assignments: 1969
## #> m/z range: 551.425088845409-1269.09515435315
## #>
## #> Peak groups having possible regisomers: 556
## #> Peak groups having possible structural functional isomers: 375
## #> 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 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