sameCEanalysis: Analysis of Single Collion Energies

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

Description

Analysis of Single Collion Energies

Usage

sameCEanalysis(pairs, nowp, nowt, sameCE, wMD = FALSE, y = 1, z = 1,
  t = 0.005, b = 0.5, replace.na = 0, sink = FALSE)

Arguments

pairs	Data frame containing the pairs which are to be compared. First column should be "pair_ID", second column "TP_ID", and the third column "par_ID".
nowp	List which contains all the MSMS spectra for the parent compounds. Output from sameCEdata function
nowt	List which contains all the MSMS spectra for the TP compounds. Output from sameCEdata function
sameCE	List which contains the measurement information for each of the collision energies. Output from sameCEdata function
wMD	Should the spectra of the TP be shifted by the mass difference of the pair? Default is FALSE
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
b	relative intensity cutoff for relCutoff(). Default is 0.05.
replace.na	value to replace NAs with. Default is 0
sink	Should the data be output into a .txt file? Default in FALSE

Value

List with the first entry the summary data frame with scores of all pairs at each collision energy. Second entry is a list, with an entry for each of the collision energies analyzed with the measurement information.

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