getCoefficients: Obtain Last-Used Score Coefficients

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

Obtain Last-Used Score Coefficients

Description

Provides the last used weight arguments from calcScores() function. Returns empty list if calcScores() has not yet been called.

Usage

getCoefficients(object)

## S4 method for signature 'metabCombiner'
getCoefficients(object)

Arguments

object

metabCombiner object

Value

A list of the last used weight parameters:

A	Specific weight penalizing feature m/z differences
B	Specific weight penalizing retention time projection error
C	Specific weight penalizing differences in abundance quantiles

Examples

data(plasma30)
data(plasma20)

p30 <- metabData(plasma30, samples = "CHEAR")
p20 <- metabData(plasma20, samples = "Red")

p.comb <- metabCombiner(p30, p20)
p.comb <- selectAnchors(p.comb, windx = 0.05, windy = 0.04, tolrtq = 0.15)
p.comb <- fit_gam(p.comb, k = 20, iterFilter = 1, family = "gaussian")
p.comb <- calcScores(p.comb, A = 90, B = 14, C = 0.5)

getCoefficients(p.comb)

hhabra/Combiner documentation built on Jan. 26, 2024, 10:30 p.m.