fit: Fitting the denoising autoencoder

In c-mertes/FRASER: Find RAre Splicing Events in RNA-Seq Data

Fitting the denoising autoencoder

Description

This method corrects for confounders in the data and fits a beta-binomial distribution to the introns/splice sites.

For more details please see FRASER.

Usage

## S3 method for class 'FraserDataSet'
fit(
  object,
  implementation = c("PCA", "PCA-BB-Decoder", "AE", "AE-weighted", "PCA-BB-full",
    "fullAE", "PCA-regression", "PCA-reg-full", "PCA-BB-Decoder-no-weights", "BB"),
  q,
  type = psiTypes,
  rhoRange = c(-30, 30),
  weighted = FALSE,
  noiseAlpha = 1,
  convergence = 1e-05,
  iterations = 15,
  initialize = TRUE,
  control = list(),
  BPPARAM = bpparam(),
  nSubset = 15000,
  minDeltaPsi = 0.1,
  ...
)

Arguments

object	A FraserDataSet object
implementation	The method that should be used to correct for confounders.
q	The encoding dimensions to be used during the fitting proceadure. Should be fitted using optimHyperParams if unknown. If a named vector is provided it is used for the different splicing types.
type	The type of PSI (jaccard, psi5, psi3 or theta for theta/splicing efficiency)
rhoRange	Defines the range of values that rho parameter from the beta-binomial distribution is allowed to take. For very small values of rho, the loss can be instable, so it is not recommended to allow rho < 1e-8.
weighted	If TRUE, the weighted implementation of the autoencoder is used
noiseAlpha	Controls the amount of noise that is added for the denoising autoencoder.
convergence	The fit is considered to have converged if the difference between the previous and the current loss is smaller than this threshold.
iterations	The maximal number of iterations. When the autoencoder has not yet converged after these number of iterations, the fit stops anyway.
initialize	If FALSE and a fit has been previoulsy run, the values from the previous fit will be used as initial values. If TRUE, (re-)initialization will be done.
control	List of control parameters passed on to optim().
BPPARAM	the BiocParallel parameters for the parallelization
nSubset	The size of the subset to be used in fitting if subsetting is used.
minDeltaPsi	Minimal delta psi of an intron to be be considered a variable intron.
...	Currently not used

Value

FraserDataSet

See Also

FRASER

c-mertes/FRASER documentation built on June 14, 2024, 7:49 p.m.