filterAnchors: Filter Outlier Ordered Pairs

In metabCombiner: Method for Combining LC-MS Metabolomics Feature Measurements

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,
  iterFilter,
  ratio,
  frac,
  bs,
  m,
  family,
  method,
  optimizer,
  loess.pars,
  ...
)

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
iterFilter	integer number of residual filtering iterations
ratio	numeric. A point is an outlier if the ratio of residual to mean residual of a fit exceeds this value. Must be greater than 1.
frac	numeric. A point is excluded if deemed a residual in more than this fraction value times the number 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
loess.pars	parameters for LOESS fitting; see ?loess.control
...	other arguments passed to mgcv::gam.

Value

anchor rts data frame with updated weights.

metabCombiner documentation built on Dec. 10, 2020, 2 a.m.