Description Usage Arguments Value

This function is a wrapper that executes all steps of `SC3`

analysis in one go.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
sc3.SingleCellExperiment(object, ks, gene_filter, pct_dropout_min,
pct_dropout_max, d_region_min, d_region_max, svm_num_cells, svm_train_inds,
svm_max, n_cores, kmeans_nstart, kmeans_iter_max, k_estimator, biology,
rand_seed)
## S4 method for signature 'SingleCellExperiment'
sc3(object, ks = NULL, gene_filter = TRUE,
pct_dropout_min = 10, pct_dropout_max = 90, d_region_min = 0.04,
d_region_max = 0.07, svm_num_cells = NULL, svm_train_inds = NULL,
svm_max = 5000, n_cores = NULL, kmeans_nstart = NULL,
kmeans_iter_max = 1e+09, k_estimator = FALSE, biology = FALSE,
rand_seed = 1)
``` |

`object` |
an object of |

`ks` |
a range of the number of clusters |

`gene_filter` |
a boolen variable which defines whether to perform gene filtering before SC3 clustering. |

`pct_dropout_min` |
if |

`pct_dropout_max` |
if |

`d_region_min` |
defines the minimum number of eigenvectors used for
kmeans clustering as a fraction of the total number of cells. Default is |

`d_region_max` |
defines the maximum number of eigenvectors used for
kmeans clustering as a fraction of the total number of cells. Default is |

`svm_num_cells` |
number of randomly selected training cells to be used
for SVM prediction. The default is |

`svm_train_inds` |
a numeric vector defining indeces of training cells
that should be used for SVM training. The default is |

`svm_max` |
define the maximum number of cells below which SVM is not run. |

`n_cores` |
defines the number of cores to be used on the user's machine. If not set, 'SC3' will use all but one cores of your machine. |

`kmeans_nstart` |
nstart parameter passed to |

`kmeans_iter_max` |
iter.max parameter passed to |

`k_estimator` |
boolean parameter, defines whether to estimate an optimal number of clusters |

`biology` |
boolean parameter, defines whether to compute differentially expressed genes, marker genes and cell outliers. |

`rand_seed` |
sets the seed of the random number generator. |

an object of `SingleCellExperiment`

class

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