autoencoderClustering.Rd
This function Compress data using autoencoder partially connected
autoencoderClustering( group = c("sudo", "docker"), scratch.folder, file, separator, nCluster, projectName, clusterMethod = c("GRIPH", "SIMLR", "SEURAT", "SHARP"), seed = 1111, pcaDimensions, permAtTime = 4, largeScale = FALSE )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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.Has to be the one in the projectName folder.Different so from the previous one. |
separator, | separator used in count file, e.g. '\t', ',' |
nCluster, | number of cluster in which the dataset is divided |
projectName, | might be different from the matrixname in order to perform different analysis on the same dataset |
clusterMethod, | clustering methods: "GRIPH","SIMLR","SEURAT","SHARP" |
seed, | important value to reproduce the same results with same input |
pcaDimensions, | number of dimensions to use for Seurat Pca reduction. |
permAtTime, | number of permutation in parallel |
largeScale, | boolean for SIMLR analysis, TRUE if rows are less then columns or if the computational time are huge |
Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
if (FALSE) { autoencoderClustering(group="docker", scratch.folder="/home/user/Riccardo/Riccardo/1_inDocker_2/scratch", file="/home/user/Riccardo/Riccardo/1_inDocker_2/data/Results/testDocker/setA.csv",separator=",", nCluster=5,clusterMethod=c("SEURAT"),seed=1111,projectName="testDocker",13, largeScale = FALSE) }