autoencoder4pseudoBulk: Autoencoder for pseudoBulk

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

Autoencoder for pseudoBulk

Description

The present function compress data using autoencoder partially connected creating pseudoBulk matrix

Usage

autoencoder4pseudoBulk(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  permutation,
  nEpochs,
  patiencePercentage = 5,
  seed = 1111,
  projectName,
  bN,
  lr = 0.01,
  beta_1 = 0.9,
  beta_2 = 0.999,
  epsilon = 1e-08,
  decay = 0,
  loss = "mean_squared_error",
  regularization = 10,
  version = 2
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder	a character string indicating the path of the scratch folder
file	a character string indicating the path of the file, with file name and extension included
separator	separator used in count file, e.g. '\t', ','
permutation	number of permutations to perform the pValue to evaluate clustering. Suggested minimal number of permutations 10
nEpochs	number of Epochs for neural network training
patiencePercentage	number of Epochs percentage of not training before to stop.
seed	important value to reproduce the same results with same input
projectName	might be different from the matrixname in order to perform different analysis on the same dataset
bN	path to the clustering.output file
lr	learning rate, the speed of learning. Higher value may increase the speed of convergence but may also be not very precise
beta_1	look at keras optimizer parameters
beta_2	look at keras optimizer parameters
epsilon	look at keras optimizer parameters
decay	look at keras optimizer parameters
loss	loss of function to use, for other loss of function check the keras loss of functions.
regularization	this parameter balances between reconstruction loss and enforcing a normal distribution in the latent space.
version	version 1 implements static batchsize, version 2 implements adaptive batchsize

Author(s)

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

kendomaniac/rCASC documentation built on June 10, 2025, 2:52 a.m.