# NOT RUN {
dbs <- list(pgdb = LipidMS::pgdb, lysopgdb = LipidMS::lysopgdb,
fadb = LipidMS::fadb, adductsTable = LipidMS::adductsTable)
candidates <- findCandidates(MS1 = LipidMS::mix_neg_fullMS, dbs[["pgdb"]],
ppm = 10, rt = c(min(MS1$RT), max(MS1$RT)), adducts = c("M-H"),
rttol = 3, dbs)
MSMS <- rbind(LipidMS::mix_neg_Ce20, LipidMS::mix_neg_Ce40)
coelfrags <- coelutingFrags(candidates$RT, MSMS, rttol)
classConf <- checkClass(candidates, clfrags = c(227.0326, 209.022, 74.0359),
clrequired = c(F, F, F, F), ftype = c("F", "F", "NL"), ppm_products = 10,
dbs)
sn1 <- chainFrags(coelfrags, chainfrags = c("lysopg_M-H"), ppm = 10,
dbs = dbs)
sn2 <- chainFrags(coelfrags, chainfrags = c("fa_M-H"), ppm = 10, dbs)
chainsComb <- combineChains(candidates, nchains=2, sn1, sn2)
intConf <- checkIntensityRules(intrules = c("lysopg_sn1/lysopg_sn1"),
rates = c("2/1"), intrequired = c(T), nchains=2, chainsComb, sn1, sn2)
res <- organizeResults(candidates, clfrags = c(227.0326, 209.022, 74.0359),
classConf, chainsComb, intrules = c("lysopg_sn1/lysopg_sn1"), intConf,
nchains = 2, class="PG")
# }
# NOT RUN {
# }
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