fit {FRASER} | R Documentation

## 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 = "psi3",
      rhoRange = c(1e-08, 1 - 1e-08),
      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 (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`

[Package FRASER version 1.4.0 Index]