filterAnchors {metabCombiner} | R Documentation

## Filter Outlier Ordered Pairs

### Description

Helper function for `fit_gam` & `fit_loess`. It filters the set of ordered pairs using the residuals calculated from multiple GAM / loess fits.

### Usage

    filterAnchors(
      rts,
      fit,
      vals,
      outlier,
      coef,
      iterFilter,
      prop,
      bs,
      m,
      family,
      method,
      optimizer,
      control,
      message,
      ...
    )

### Arguments

`rts` | Data frame of ordered retention time pairs.
`fit` | Either "gam" for GAM fits, or "loess" for loess fits
`vals` | numeric values: k values for GAM fits, spans for loess fits
`outlier` | Thresholding method for outlier dection. If "MAD", the threshold is the mean absolute deviation (MAD) times `coef`; if "boxplot", the threshold is `coef` times IQR plus 3rd quartile of a model's absolute residual values.
`coef` | numeric (> 1) multiplier for determining thresholds for outliers (see `outlier` argument)
`iterFilter` | integer number of outlier filtering iterations
`prop` | numeric. A point is excluded if deemed a residual in more than this proportion of fits. Must be between 0 & 1.
`bs` | character. Choice of spline method from mgcv; either "bs" or "ps"
`m` | integer. Basis and penalty order for GAM; see ?mgcv::s
`family` | character. Choice of mgcv family; see: ?mgcv::family.mgcv
`method` | character. Smoothing parameter estimation method; see: ?mgcv::gam
`optimizer` | character. Method to optimize smoothing parameter; see: ?mgcv::gam
`control` | control parameters for loess fits; see: ?loess.control
`message` | Option to print message indicating function progress
`...` | other arguments passed to `mgcv::gam`.

### Value

anchor rts data frame with updated weights.

[Package metabCombiner version 1.4.0 Index]