searchAnalyte: Analyte detection in an MSI dataset

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

Analyte detection in an MSI dataset

Description

This function check if an analyte (given by m/z) is detectable in the MS data represented by a 'sparseIntensityMatrix' object.

Usage

searchAnalyte(
  m,
  fwhm,
  spData,
  wMethod = "Gaussian",
  spwin = NA,
  verifiedMasses = NA,
  confirmedOnly = FALSE,
  metaData = list()
)

Arguments

m	the mass to be queried (in Da).
fwhm	the fwhm at 'm'.
spData	an S3 object of type 'sparseIntensityMatrix' holding the sparse MSI data.
wMethod	wighting method; c("Gaussian", "sum", "max", "mean").
spwin	optional, an object of type 'owin'. If not given the function tries to generate the spatial window out of the coordinates of all points of the dataset stored in 'spData' (default behavior).
verifiedMasses	an optional numeric vector of m/z values that are (externally) verified to be real molecular entities with a certain confidence, ex. 'mz' column of a METASPACE annotation result.
confirmedOnly	if 'TRUE', returns detections only if confirmed by 'verifiedMasses'.
metaData	optional named list with additional identifiers for the analyte under study, ex. list(lipidID = "..", sumformular = "..", ..). This will be passed to the 'metaData' slot of the resulting 'analytePointPattern' object.

Value

An analyte point patter of type 'ppp' and 'analytePointPattern' containing the hits for 'm' in 'msData'. If 'confirmedOnly = TRUE' then only these hits are returned.

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