combineChains {LipidMS} | R Documentation |
It calculates combinations of chain fragments that sum up the same number of carbons and double bounds as the precursor.
combineChains(candidates, nchains, sn1, sn2, sn3, sn4)
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. |
List of data frames with candidate chains structures.
M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
library(LipidMSdata) dbs <- assignDB() candidates <- findCandidates(MS1 = MS1_neg$peaklist, db = dbs$pgdb, ppm = 10, rt = c(0, 2000), adducts = c("M-H"), rttol = 10, dbs = dbs, rawData = MS1_neg$rawScans, coelCutoff = 0.8) MSMS <- rbind(MSMS1_neg$peaklist, MSMS2_neg$peaklist) rawData <- rbind(MS1_neg$rawScans, MSMS1_neg$rawScans, MSMS2_neg$rawScans) coelfrags <- coelutingFrags(candidates, MSMS, rttol = 10, rawData = rawData, coelCutoff = 0.8) sn1 <- chainFrags(coelfrags, chainfrags = c("lysopg_M-H"), ppm = 10, candidates = candidates, dbs = dbs) sn2 <- chainFrags(coelfrags, chainfrags = c("fa_M-H"), ppm = 10, candidates = candidates, dbs = dbs) chainsComb <- combineChains(candidates, nchains=2, sn1 = sn1, sn2 = sn2) intConf <- checkIntensityRules(intrules = c("lysopg_sn1/lysopg_sn1"), rates = c("2/1"), intrequired = c(TRUE), nchains=2, chainsComb)