LipidMS (version 1.0.0)

checkIntensityRules: Check intensity rules

Description

Check intensity rules to confirm chains position.

Usage

checkIntensityRules(intrules, rates, intrequired, nchains, combinations)

Arguments

intrules

character vector specifying the fragments to compare. See details.

rates

character vector with the expected rates between fragments given as a string (i.e. "3/1"). See details.

intrequired

logical vector indicating if any of the rules is required. If not, at least one must be verified to confirm the structure.

nchains

number of chains of the targeted lipid class.

combinations

output of combineChains.

Value

List of logical vectors with the confirmation for each combination.

Details

This function will be employed when the targeted lipid class has more than one chain.

Taking PG subclass as an example, intensities of lysoPG fragments (informative for sn1) can be employed to confirm the chains structure (intrules = c("lysopg_sn1/lysopg_sn1")). In this case, the intensity of the lysoPG resulting from the loss of the FA chain in sn2 is at least 3 times greater (rates = c("3/1")) than the lysoPG resulting from the loss of the FA chain in sn1.

For the intrules argument, "/" will be use to separate the fragments related to each chain (sn1/sn2/etc), and "_" will be use to indicate the list in which they'll be searched. This will depend on the chain fragments rules defined previously. Following the example, as we use lysoPG to define the sn1 position, both fragments will be searched in this list (sn1).

For classes with more than one FA chain, if some intensity rule should be employed to identify their position but they are no defined yet, use "Unknown". If it is not necessary because the fragmentation rules are informative enough to define the position (i.e. sphingolipid species), just leave an empty vector.

Examples

# NOT RUN {
dbs <- assignDB()

candidates <- findCandidates(MS1 = LipidMS::MS1_neg$peaklist,
db = dbs$pgdb, ppm = 10, rt = c(0, 2000), adducts = c("M-H"),
rttol = 10, rawData = MS1_neg$rawScans, coelCutoff = 0.8)

MSMS <- rbind(LipidMS::MSMS1_neg$peaklist, LipidMS::MSMS2_neg$peaklist)
rawData <- rbind(LipidMS::MS1_neg$rawScans, LipidMS::MSMS1_neg$rawScans,
LipidMS::MSMS2_neg$rawScans)
coelfrags <- coelutingFrags(candidates$RT, MSMS, rttol = 10, rawData = rawData,
coelCutoff = 0.8)

sn1 <- chainFrags(coelfrags, chainfrags = c("lysopg_M-H"), ppm = 10,
dbs = dbs)
sn2 <- chainFrags(coelfrags, chainfrags = c("fa_M-H"), ppm = 10, dbs = 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)
# }
# NOT RUN {
# }