checkIntRules: Check intensity rules
In LipidMS: Lipid Annotation for LC-MS/MS DDA or DIA Data

checkIntRules

R Documentation

Check intensity rules

Description

Check intensity rules to confirm chains structure.

Usage

checkIntRules(intrules, rates, intrequired, nchains, combinations, sn)

Arguments

`intrules`	character vector specifying the fragments to compare. See details.
`rates`	character vector with the expected rates 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
`sn`	list of chain fragments identified. Object fragments of the combineChains output.

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 lysoPG resulting from the loss of the FA chain in sn2 is at least 3 times higher (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 to compare, and "_" will be use to indicate in which list of fragments we need to look for their intensities. This will depend on the chain fragments rules defined previiously.