Permutations and Clustering

This function executes a ubuntu docker that produces a specific number of permutation to evaluate clustering.

clusterStability(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  range1 = 3,
  range2 = 3,
  separator,
  logTen = 0,
  clustering,
  perplexity = 10,
  pcaDimensions,
  seed = 1111
)

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

nPerm,

number of permutations to perform the pValue to evaluate clustering

range1,

first number of cluster for k means algorithm

range2,

last number of cluster for k means algorithm

separator,

separator used in count file, e.g. '\t', ','

logTen,

1 if the count matrix is already in log10, 0 otherwise

clustering,

clustering method to use : "SIMLR" , "tSne", "griph"

perplexity,

Number of close neighbors for each point. This parameter is specific for tSne. Default value is 10.Setting this parameter when use a clustering method different by tSne will be ignored.

pcaDimensions,

dimensions to use for pca reduction for Seurat

seed,

important value to reproduce the same results with same input

Value

plot with cluster stability

Author

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

Examples

if (FALSE) {
}