Description Usage Arguments Value See Also

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`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
## 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,
...
)
``` |

`object` |
A |

`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 |

`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 |

`FraserDataSet`

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