organizeResults {LipidMS} | R Documentation |
Prepare a readable output for LipidMS identification functions.
organizeResults( candidates, clfrags, classConf, chainsComb, intrules, intConf, nchains, class )
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.). |
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) 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")