`clusterNgriph.Rd`

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 )

group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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 |

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

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