mzFit: Compute m/z Shift Model

View source: R/calcScores.R

mzFitR Documentation

Compute m/z Shift Model


Generates a GAM model for correcting systematic m/z shifts observed between a pair of LC-MS data sets.


mzFit(object, fit = mzfitParam(), plot = TRUE, ...)



metabCombiner object


List of m/z shift parameter values; see ?mzfitParam


Logical. Option to plot the m/z shift model.


other arguments to be passed to plot


Correcting for systematic m/z shifts improves the scores for feature pair alignments, yielding more accurate match hypotheses. This function generates a basis spline curve, modeling the m/z shift (mzy - mzx) as a function of m/z (mzx). Selected points are ordered feature pairs that meet criteria for m/z, RT (rty vs rtProj), and Q tolerances set in the mzfit list argument (see: mzfitParam). If

Setting the plot option to TRUE generates an image of the curve fit through the selected points and is a useful method for determining if m/z mapping is appropriate for the analysis and tuning certain parameters.

This function is called within calcScores, which can help improve the pairwise scores


model object of class gam or 0 (if no model selected)



p30 <- metabData(plasma30, samples = "CHEAR")
p20 <- metabData(plasma20, samples = "Red", rtmax = 17.25)
p.comb <- metabCombiner(xdata = p30, ydata = p20, binGap = 0.0075)

p.comb <- selectAnchors(p.comb, tolmz = 0.003, tolQ = 0.3, windy = 0.02)
p.comb <- fit_gam(p.comb, k = 20, iterFilter = 1, family = "gaussian")

mzmodel <- mzFit(p.comb, plot = TRUE,
                 fit = mzfitParam(mz = 0.003, rt = 0.03, Q = 0.3, k = 20))

hhabra/Combiner documentation built on June 5, 2024, 10:56 a.m.