organizeResults {LipidMS}

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.

Author(s)

M Isabel Alcoriza-Balaguer <[e-mail]>