calcScoresParam: List calcScores Defaults

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

List calcScores Defaults

Description

List of default parameters for score calculation step of main package workflow. See help(calcScores) or ?calcScores for details.

Usage

calcScoresParam(
  A = 75,
  B = 10,
  C = 0.25,
  fit = "gam",
  groups = NULL,
  usePPM = FALSE,
  useAdduct = FALSE,
  adduct = 1.25,
  brackets_ignore = c("(", "[", "{")
)

Arguments

A	m/z difference specific weight; default: 75
B	RT prediction error specific weight; default: 10
C	Q difference specific weight; default: 0.25
fit	choice of fitted model ("gam" or "loess"); default: "gam"
groups	choice of m/z groups to score
usePPM	choice to use PPM for m/z differences; default: FALSE
useAdduct	choice to use adduct strings in scoring; default: FALSE
adduct	value divisor for mismatched adduct strings; default: 1.25
brackets_ignore	bracket types for ignoring string comparisons

Value

list of calcScores parameters

See Also

calcScores, metabCombine

Examples

cs_param <- calcScoresParam(A = 60, B = 15, C = 0.3)

cs_param <- calcScoresParam(A = 0.1, B = 20, C = 0.2, usePPM = TRUE)

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