`genesPrioritization.Rd`

This function executes a ubuntu docker that produces a specific number of permutation to evaluate clustering and identify the genes that play the major role in clustering.

genesPrioritization( group = c("sudo", "docker"), scratch.folder, file, nPerm, permAtTime, percent, nCluster, separator, logTen = 0, seed = 111, sp = 0.8, clusterPermErr = 0.05 )

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 be executed |

permAtTime, | number of permutations computed in parallel |

percent, | percentage of random cells removed in each permutation |

nCluster, | the number of clusters, where to run prioritization |

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 |

sp, | minimun number of percentage of cells that has to be in common in a cluster, between two permutations, default 0.8 |

clusterPermErr, | probability error in depicting the number of clusters in each permutation, default = 0.05 |

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.

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

if (FALSE) { system("wget http://130.192.119.59/public/section4.1_examples.zip") unzip("section4.1_examples.zip") setwd("section4.1_examples") genesPrioritization(group="docker",scratch.folder="/data/scratch/",file=paste(getwd(), "bmsnkn_5x100cells.txt", sep="/"), nPerm=160, permAtTime=8, percent=10, nCluster=5, separator="\t", logTen=0, seed=111, sp=0.8, clusterPermErr=0.05) }