fragCountSim: Wrapper function

In dutchjes/MSMSsim: Functions for processing HRMS2 spectra from output from RMassBank, mainly for calculating spectral similarity

Description

Calculates similarity score of two MSMS spectra using count of matched fragments

Usage

fragCountSim(spec.top, spec.bottom, y = 0, z = 1, t = 0.005,
  replace.na = 0, b = 0.05, min.frag = 0)

Arguments

spec.top	MSMS spectrum 1
spec.bottom	MSMSpectrum 2
y	m/z weighting factor for simTableWeighting(). Default is 0
z	intensity weighting factor for simTableWeighting(). Default is 1
t	m/z tolerance for merging factors for simTable(). Default is 0.005
replace.na	value to replace NAs with. Default is 0
b	relative intensity cutoff for relCutoff(). Default is 0.05.
min.frag	the minimum number of matched fragments required. If number of matched fragments is less than this value, score is automatically 0. Default is 0

Value

List with the the similarity score (sum of number of matched fragments) and data frame showing output from each step (i.e., merging and intensity cutoff). First column is m/z, then the top and bottom weighted values used for the similarity score calculation. Fourth and fifth columns show the result after applying the relative intensity cutoff, followed by if fragments are matching. Final two column show the original input intensities prior to any processing.

dutchjes/MSMSsim documentation built on June 29, 2019, 12:12 a.m.