LipidMS (version 3.0.0)

combineChains: Combine chain fragments that could belong to the same precursor.

Description

It calculates combinations of chain fragments that sum up the same number of carbons and double bounds as the precursor.

Usage

combineChains(candidates, nchains, sn1, sn2, sn3, sn4)

Arguments

candidates

candidates data frame. Output of findCandidates.

nchains

number of chains of the targeted lipid class.

sn1

list of chain fragments identified for sn1 position. Output of chainFrags.

sn2

list of chain fragments identified for sn2 position. Output of chainFrags. If required.

sn3

list of chain fragments identified for sn3 position. Output of chainFrags. If required.

sn4

list of chain fragments identified for sn4 position. Output of chainFrags. If required.

Value

List of data frames with candidate chains structures.

Examples

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

library(LipidMS)
dbs <- assignDB()

MS1 <- LipidMSdata2::msobjectDIAneg$peaklist$MS1
MS1 <- MS1[MS1$isotope %in% c("[M+0]"), !colnames(MS1) %in% c("isotope", "isoGroup")]
MS2 <- LipidMSdata2::msobjectDIAneg$peaklist$MS2[,c("mz", "RT", "int", "peakID")]
rawData <- rbind(LipidMSdata2::msobjectDIAneg$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)
# }
# NOT RUN {
# }