`clusterStability.Rd`

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

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

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 the pValue to evaluate clustering |

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. |

pcaDimensions, | dimensions to use for pca reduction for Seurat |

seed, | important value to reproduce the same results with same input |

plot with cluster stability

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

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