organizeResults: Prepare output for LipidMS annotation functions
In LipidMS: Lipid Annotation for LC-MS/MS DDA or DIA Data

View source: R/subfunctionsIdentification.R

organizeResults

R Documentation

Prepare output for LipidMS annotation functions

Description

Prepare a readable output for LipidMS identification functions.

Usage

organizeResults(
  candidates,
  coelfrags,
  clfrags,
  classConf,
  chainsComb,
  intrules,
  intConf,
  nchains,
  class,
  acquisitionmode
)

Arguments

`candidates`	candidates data frame. Output of findCandidates.
`coelfrags`	list of coeluting fragments for each candidate
`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.).
`acquisitionmode`	acquisition mode (DIA or DDA).

Details

Coelution score for DIA data is calculated as the mean coelution score of all fragments used for annotation, while for DDA data, the intensity score is given, which is calculated as the sum of the relative intensities of the fragments used for annotation.