calcScoresParam {metabCombiner} | R Documentation

## 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)

[Package metabCombiner version 1.4.0 Index]