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)
}
```