mzfitParam: Parameterize m/z Shift Model

In hhabra/Combiner: Method for Combining LC-MS Metabolomics Feature Measurements

Parameterize m/z Shift Model

Description

Return a list of parameters for computing a m/z shift model between a pair of LC-MS metabolomics data sets.

Usage

mzfitParam(mz = 0.003, rt = 0.03, Q = 0.3, k = 10)

Arguments

mz	Numeric. Limits the m/z distance between feature pairs for modeling
rt	Numeric. Limits the RT distance between feature pairs for modeling (note: this is proportion of total retention time)
Q	Numeric. Limits the Q distance between feature pairs for modeling
k	integer k value controlling the dimension of the basis spline fit

Details

Correcting for systematic m/z shifts improves the scores for feature pair alignments, yielding more accurate match hypotheses. This function yields a parameter list for GAM spline fitting of points that meet criteria for m/z, RT (rty vs rtProj), and Q tolerances. The number of knots for the GAM fit is controlled by hyperparameter k.

Value

list of parameter values

Examples

mzfit <- mzfitParam(mz = 0.003, rt = 0.05, Q = 0.2, k = 20)

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