findfeature: findfeature

In cbroeckl/RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

findfeature

Description

see if any features match a given mass, and whether they are plausibly M0

Usage

findfeature(
  ramclustObj = NULL,
  mz = NULL,
  mztol = 0.02,
  rt = NULL,
  rttol = 2,
  iso.rttol = 2,
  zmax = 6,
  m.check = TRUE
)

Arguments

ramclustObj	R object: the ramclustR object to explore
mz	numeric: mz value to search for
mztol	numeric: absolute mass tolerance around mz
rt	numeric: optional rt value to search for (generally in seconds, though use whatever units your data is in)
rttol	numeric: absolute retention time tolerance around rt.
iso.rttol	numeric: when examining isotope patterns, feature retention time tolerance around features matching mz +- mztol
zmax	integer: maximum charge state to consider. default is 6.
m.check	logical: check whether the matching masses are plausibly M0. That is, we look for ions 1 proton mass (from charge state 1:zmax) below the target m/z at the same time that have intensities consistent with target ion being a non-M0 isotope.

Details

a convenience function to perform a targeted search of all features for a mass of interest. Also performs a crude plausibility check as to whether the matched feature could be M0, based on the assumption of approximately 1 carbon per 17 m/z units and natural isotopic abundance of 1.1

Value

returns a table to the console listing masses which match, their retention time and intensity, and whether it appears to be plausible as M0

Author(s)

Corey Broeckling

cbroeckl/RAMClustR documentation built on Sept. 1, 2024, 1:50 a.m.