autoencoderClustering | R Documentation |
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 |
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
## Not run:
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)
## End(Not run)
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