deepClustering

The present function compress data using autoencoder partially connected

deepClustering(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  nCluster,
  bias,
  finetune_iters = 1e+05,
  nEpochs = 50000,
  seed = 1111,
  projectName,
  bN = "NULL"
)

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', ','

nCluster,

number of cluster in which the dataset is divided

bias,

bias method to use : "mirna" , "TF", "CUSTOM", kinasi,immunoSignature, cytoBands, ALL

finetune_iters,

number of deep iteration

nEpochs,

number of Epochs for neural network training

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,

name of the custom bias file. This file need header, in the first column has to be the source and in the second column the gene symbol. All path needs to be provided.

Author

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

Examples

if (FALSE) {
deepClustering(group=c("docker"), scratch.folder="/scratch/", file="/home/lucastormreig/clustering_autoencoder/DCA/Rfunction/setA2.csv",separator=",", nCluster=5, bias="TF", finetune_iters=3, nEpochs=2,seed=1111,projectName="TF",bN="NULL")
}