findmass: findmass

In sneumann/RAMClustR: RAMClust: a novel feature clustering method enables spectral-matching based annotation for metabolomics data

Description

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

Usage

findmass(ramclustObj = RC, mz = NULL, mztol = 0.02, 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
rttol	numeric: when examining isotope patterns, feaure 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 feaures 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 isottopic 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

sneumann/RAMClustR documentation built on May 30, 2019, 5:05 a.m.