searchLipid: Find lipids in MSI datasets

In CeMOS-Mannheim/moleculaR: Spatial Probabilistic Mapping of Metabolite Ensembles in Mass Spectrometry Imaging

Find lipids in MSI datasets

Description

This function check if a deprotonated/protonated or any alkali version lipid is detectable in the MS data represented by a sparse matrix.

Usage

searchLipid(
  m,
  fwhm,
  massAxis,
  spData,
  coords,
  mtspc = NA,
  confirmedOnly = FALSE,
  adduct = NA,
  mode = NA,
  modeAdduct = NA,
  lipidID = NA,
  sumformula = NA,
  abbrev = NA,
  numDoubleBonds = NA
)

Arguments

sumformula	for internal use only.
abbrev	for internal use only.
numDoubleBonds	for internal use only.
m:	the mass to be queried (Da).
fwhm:	the fwhm at 'm'.
massAxis:	the mass axis of the whole MS dataset to be searched against.
spData:	the sparse matrix containing the negative or poisitive ion mode info.
coords:	the coordinates of spectra contained within the spData.
mtspc:	a data frame of the metaspcae identifications.
confirmedOnly:	if TRUE, returns detections only if confirmed by metaspace.
lipidID:	for internal use only.
fullName	for internal use only.

Value

A dataframe containing the hits for 'm' in 'msData'.

CeMOS-Mannheim/moleculaR documentation built on April 14, 2025, 8:27 a.m.