fitloessParam: List fitLoess Defaults

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

List fitLoess Defaults

Description

List of default parameters for loess fitting step of main package workflow, See help(fit_loess) or ?fit_loess for more details.

Usage

fitloessParam(
  useID = FALSE,
  spans = seq(0.2, 0.3, by = 0.02),
  outlier = "MAD",
  coef = 2,
  iterFilter = 2,
  prop = 0.5,
  weights = 1,
  message = TRUE,
  rtx = c("min", "max"),
  rty = c("min", "max"),
  control = loess.control(surface = "direct", iterations = 10)
)

Arguments

useID	choice of preserving identity-based anchors; default: FALSE
spans	values for span parameter which controls degree of smoothing
outlier	outlier filtering method (either "MAD" or "boxplot"); default: "MAD"
coef	outlier filtering coefficient; default: 2
iterFilter	number of outlier filtering iterations; default: 2
prop	minimum proportion of fits where a point can be a flagged outlier; default: 0.5
weights	optional supplied weights to individual points; default: 1
message	option to print progress message; default: TRUE
rtx	ordered pair of endpoints for rtx; default: ("min", "max")
rty	ordered pair of endpoints for rty; default: ("min", "max")
control	loess-specific control parameters; see: ?loess.control

Value

list of fit_loess parameters:

See Also

fit_loess, metabCombine

Examples

fitParam <- fitloessParam(spans = c(0.2,0.25,0.3), outlier = "boxplot",
                         iterFilter = 3, coef = 1.5, message = FALSE,
                         control = loess.control(iterations = 4))

hhabra/Combiner documentation built on Jan. 26, 2024, 10:30 p.m.