makeEdges: makeEdges

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

Description

Make an edgelist (data.frame) using a vector of parentmasses and a list of MS spectra. Wrapper for network1().

Usage

makeEdges(speclist, parentmasses = NULL, mztol = 0.005,
  method = "cosine", minpeaks = 6, nonmatched = T)

Arguments

speclist	(non-nested) list of MS spectra
parentmasses	vector of parent m/z values (same length as speclist).
mztol	max difference between matched peaks in m/z
method	"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

Details

Columns of the returned data.frame:

• from vertex id

• to vertex id

• cosine similarity measure

• deltamz parent mass difference

Value

a data.frame with edge information, see Details

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