filterAnchors: Filter Outlier Ordered Pairs

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

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.

hhabra/metabCombiner documentation built on Jan. 26, 2024, 12:23 p.m.