Defining with griph the range of number of clusters to be used with SIMLR

This function executes a ubuntu docker that produces a specific number of permutation to evaluate the range of optimal number of clusters using griph algorithm. For more info see rCASC vignette.

clusterNgriph(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  permAtTime,
  percent,
  separator,
  logTen = 0,
  seed = 111
)

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
permAtTime,: number of permutations that can be computed 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

Value

A folder Results containing a folder with the name of the experiment, which contains: VioPlot of silhouette cells value for each number of cluster used, a folder with the number of clusters selected as optimal by griph, which contains: 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, hist.pdf describing the number of times a specific number of clusters was used during permutations

Author

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

Examples

if (FALSE) {
 clusterNgriph(group="docker",scratch.folder="/data/scratch/",file=paste(getwd(), "bmsnkn_5x100cells.txt", sep="/"), nPerm=16, permAtTime=8, percent=10, separator="\t",logTen=0, seed=111)
}