Echidna_vae_generate: Simulate B or T cell receptor sequences by variational...

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Simulate B or T cell receptor sequences by variational autoencodes(VAEs) trained with experimental data.

Description

Simulate B or T cell receptor sequences by variational autoencodes(VAEs) trained with experimental data.

Usage

Echidna_vae_generate(
  sequence,
  n.train,
  n.sample,
  batch.size,
  latent.dim,
  intermediate.dim,
  epochs,
  epsilon.std,
  null.threshold
)

Arguments

sequence	a vector of seuqnece the model to be trained on
n.train	number of sequence to be used in training set, the rest will be in testing set
n.sample	number of new sequence to generate from VAE model
batch.size	set to larger to save time, set to smaller to same computing power
latent.dim	parameter used in VAE model
intermediate.dim	parameter used in VAE model
epochs	parameter used in VAE model
epsilon.std	parameter used in VAE model
null.threshold	threshold of predicted value to be considered as an existing base, default is 0.05. When generated sequence is too short, lower this threshold.

Value

A simulated VDJ repertoire on the basis of the input experimental repertoire

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.