estimate.hyperparameters: estimate.hyperparameters

In microbiome/RPA: RPA: Robust Probabilistic Averaging for probe-level analysis

estimate.hyperparameters

Description

Hyperparameter estimation.

Usage

estimate.hyperparameters(
  sets = NULL,
  probe.parameters = list(alpha = 2, beta = 1),
  batches,
  cdf = NULL,
  bg.method = "rma",
  epsilon = 0.01,
  load.batches = FALSE,
  save.hyperparameter.batches = FALSE,
  mc.cores = 1,
  verbose = TRUE,
  normalization.method = "quantiles",
  save.batches.dir = ".",
  unique.run.identifier = NULL,
  set.inds = set.inds
)

Arguments

sets	Probesets to handle. All probesets by default.
probe.parameters	User-defined priors. May also include quantile.basis
batches	Data batches for online learning
cdf	CDF probeset definition file
bg.method	Background correction method
epsilon	Convergence parameter
load.batches	Logical. Load preprocessed data whose identifiers are picked from names(batches). Assuming that the same batch list (batches) was used to create the files in online.quantiles function.
save.hyperparameter.batches	Save hyperparameters for each batch into files using the identifiers with batch name with -hyper.RData suffix.
mc.cores	Number of cores for parallel computation
verbose	Print progress information
normalization.method	Normalization method
save.batches.dir	Specify the output directory for temporary batch saves.
unique.run.identifier	Define identifier for this run for naming the temporary batch files. By default, a random id is generated.
set.inds	Probeset indices

Value

alpha: Hyperparameter alpha (same for all probesets); betas: Hyperparameter beta (probe-specific); variances: Probe-specific variances (beta/alpha)

Author(s)

Leo Lahti [e-mail]

References

See citation("RPA")

Examples

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microbiome/RPA documentation built on April 9, 2023, 10:59 a.m.