getOptimalLowessFvalue: Optimal Selection of the LOWESS Bandwidth Parameter Using the...

In adele/omicsMA: Variance-Preserving Estimation and Normalization of M-A Values

Optimal Selection of the LOWESS Bandwidth Parameter Using the HRCp Criterion

Description

LOWESS parameter selection method, proposed by \insertCiteribeiro2019omicsMAomicsMA, that is parsimonious and considers intrinsic characteristics of microarray data, such as heteroskedasticity. Particularly, the best bandwidth is selected according to the HRCp criterion \insertCiteliu2013heteroscedasticityomicsMA.

Usage

getOptimalLowessFvalue(M.mean, A.mean, eva.values = seq(0.2, 1, by =
  0.05), debug = TRUE, save.objs = TRUE, save.plots = TRUE,
  dir.to.save = "./", array.id = "array")

Arguments

M.mean	A numeric vector with the M values for the p genes.
A.mean	A numeric vector with the A values for the p genes.
eva.values	A numeric vector with bandwith values to be considered by the LOWESS parameter selection method.
debug	A logical value indication if you want to view logs of the execution.
save.objs	A logical value indicating if you want to save objects with partial results.
save.plots	A logical value indicating if you want to generate the M plots illustrating the bandwidth parameter selection process.
dir.to.save	Path to the folder you want to save the output objects.
array.id	A character string identifying the array.

Value

A list with the following elements:

opt.value

The optimal bandwith.

criterion.val

A list with the mean square errors for the estimates obtained for each evaluated bandwith.

criterion.df

A list with the effective degrees of freedom for the estimates obtained for each evaluated bandwith.

fits

A list with the estimates obtained for each evaluated bandwith.

References

\insertAllCited

adele/omicsMA documentation built on July 4, 2025, 3:49 a.m.