network1: network1

In mjhelf/MassTools: R package for mass and molecular formula calculations

Description

Compare two spectra and calculate a similarity score (e.g. intensity values of matched MS peaks) NOTE: handling matching peaks from one spectrum that match multiple peaks from the other spectrum is implemented now but needs testing

Usage

network1(spec1, spec2, mztol = 0.005, ppm = 0, parentshift = 0,
  method = "cosine", minpeaks = 6, nonmatched = T)

Arguments

spec1	spectrum 1
spec2	spectrum 2
mztol	max m/z difference between peaks to match matching
ppm	max difference between peaks in ppm
parentshift	m/z difference between parentmasses (importantly, has to be Parent(spec2) - Parent(spec1) ) to find alternative matches / neutral loss matches; will only be calculated if abs(parentshift) > abs(mztol)
method	method passed on to pairCompare(); "cosine" will use lsa::cosine(), "pearson" will use stats::cor()
minpeaks	minimum number of peaks that have to be matched, otherwise returns 0
nonmatched	if TRUE, will add non-matching peaks to calculation, with 0 intensity in the spectrum missing the peak

Value

the result of the method call, a numeric similarity score

mjhelf/MassTools documentation built on Nov. 19, 2021, 2:38 a.m.