Permutations and Clustering — permutationClusteringSHARP • rCASC

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

permutationClusteringSHARP(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  permAtTime,
  percent,
  separator,
  logTen = 0,
  seed = 1111,
  perplexity = 10
)

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
separator,: separator used in count file, e.g. '\t', ','
logTen,: 1 if the count matrix is already in log10, 0 otherwise
seed,: important value to reproduce the same results with same input
perplexity,: number of close neighbors for each point. This parameter is specific for tSne. Default value is 10. the performance of t-SNE is fairly robust under different settings of the perplexity. The most appropriate value depends on the density of your data. A larger/denser dataset requires a larger perplexity. Typical values for the perplexity range between 5 and 50

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) {
 permutationClusteringSHARP(group="docker",scratch.folder="/home/lucastormreig/CASC2.0/permutationClustering/scratch/",file="/home/lucastormreig/CASC2.0/permutationClustering/Data/TOTAL.csv",nPerm=4,permAtTime=2,percent=10,3,4,separator=",",logTen=0, perplexity, seed=1111)
}