LipidMS (version 2.1.2)

organizeResults: Prepare output for LipidMS annotation functions

Description

Prepare a readable output for LipidMS identification functions.

Usage

organizeResults(
  candidates,
  clfrags,
  classConf,
  chainsComb,
  intrules,
  intConf,
  nchains,
  class,
  acquisitionmode
)

Arguments

candidates

candidates data frame. Output of findCandidates.

clfrags

vector containing the expected fragments for a given lipid class.

classConf

output of checkClass

chainsComb

output of combineChains

intrules

character vector specifying the fragments to compare. See checkIntensityRules.

intConf

output of checkIntensityRules

nchains

number of chains of the targeted lipid class.

class

character value. Lipid class (i.e. PC, PE, DG, TG, etc.).

acquisitionmode

character value. DIA or DDA.

Examples

# NOT RUN {
devtools::install_github("maialba3/LipidMSdata2")

library(LipidMS)
dbs <- assignDB()

MS1 <- LipidMSdata2::msobjectDIAneg$peaklist$MS1
MS1 <- MS1[MS1$isotope %in% c("[M+0]"), !colnames(MS1) %in% c("isotope", "group")]
MS2 <- LipidMSdata2::msobjectDIAneg$peaklist$MS2[,c("m.z", "RT", "int", "peakID")]
rawData <- rbind(LipidMSdata2::msobjectDIAneg$MS1, LipidMSdata2::msobjectDIAneg$MS2)

candidates <- findCandidates(MS1 = MS1, db = dbs$pgdb, ppm = 10,
rt = c(0, 2000), adducts = c("M-H"), rttol = 10, dbs = dbs,
rawData = rawData, coelCutoff = 0.8)
coelfrags <- coelutingFrags(candidates, MSMS, rttol = 10, rawData = rawData,
coelCutoff = 0.8)
classConf <- checkClass(candidates, coelfrags,
clfrags = c(227.0326, 209.022, 74.0359),
clrequisites = c(FALSE, FALSE, FALSE, FALSE),
ftype = c("F", "F", "NL"), ppm = 10, dbs = dbs)
sn1 <- chainFrags(coelfrags, chainfrags = c("lysopg_M-H"),
candidates = candidates, ppm = 10, dbs = dbs)
sn2 <- chainFrags(coelfrags, chainfrags = c("fa_M-H"), ppm = 10,
candidates = candidates, dbs = dbs)
chainsComb <- combineChains(candidates, nchains=2, sn1, sn2)
intConf <- checkIntensityRules(intrules = c("lysopg_sn1/lysopg_sn1"),
rates = c("2/1"), intrequired = c(TRUE), nchains=2, chainsComb)

res <- organizeResults(candidates, clfrags = c(227.0326, 209.022, 74.0359),
classConf, chainsComb, intrules = c("lysopg_sn1/lysopg_sn1"), intConf,
nchains = 2, class="PG", acquisitionmode = msobject$metaData$generalMetadata$acquisitionmode)
# }
# NOT RUN {

# }