View source: R/autoencoder4Pseudobulk.R
autoencoder4pseudoBulk | R Documentation |
The present function compress data using autoencoder partially connected creating pseudoBulk matrix
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
)
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 |
Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.