Autoencoder4clustering

The present function compress data using autoencoder partially connected

autoencoderDB(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  permutation,
  nEpochs,
  patiencePercentage = 5,
  seed = 1111,
  projectName,
  lr = 0.01,
  loss = "mean_squared_error"
)

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

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

lr,

learning rate, the speed of learning. Higher value may increase the speed of convergence but may also be not very precise

loss,

loss of function to use, for other loss of function check the keras loss of functions.

Author

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

Examples

if (FALSE) {
}