Permutations and Clustering

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

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

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

permAtTime,

number of permutations that can be computes in parallel

percent,

percentage of randomly selected cells removed in each permutation

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.

seed,

important value to reproduce the same results with same input

rK,

1 for rankGene algorithm 0 otherwise WARNING, very slow with this feature. This parameter is specific for SIMLR. Setting this parameter to 1 with other clustering methods will not give any different result to set the parameter to 0.

Value

VioPlot of silhouette cells value for each number of cluster used,clusterP file with clustering results for each permutation, killedCell file with removed cells in each permutation, clustering.output a sommarize file with general information for each cells.

Author

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

Examples

if (FALSE) {
 permutationClustering("docker","/home/lucastormreig/CASC2.0/permutationClustering/scratch/","/home/lucastormreig/CASC2.0/permutationClustering/Data/TOTAL.csv",4,2,10,3,4,separator=",",logTen=0,clustering="SIMLR",perplexity=0)
}