`ti_celltrails.Rd`

Will generate a trajectory using CellTrails.

This method was wrapped inside a container. The original code of this method is available here.

ti_celltrails(filter_features = FALSE, threshold_dl = 2L, threshold_cov = 0.05, threshold_ff = 1.7, min_expr = 0L, frac = 100L, min_size = 0.01, min_feat = 5L, max_pval = 1e-04, min_fc = 2L, l = 10L)

filter_features | Whether to include celltrails feature filtering. Default: FALSE. Format: logical. |
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threshold_dl | Minimum number of samples; if value < 1 it is interpreted as fraction, otherwise as absolute sample count. Domain: U(0, 100). Default: 2. Format: integer. |

threshold_cov | Minimum coefficient of variation; numeric value between 0 and 1. Domain: U(0, 1). Default: 0.05. Format: numeric. |

threshold_ff | A Z-score cutoff. Domain: U(0, 5). Default: 1.7. Format: numeric. |

min_expr | Minimum average feature expression. Domain: U(0, 2). Default: 0. Format: numeric. |

frac | Fraction or number (if frac > 1) of eigengaps used to perform linear fit. Domain: e^U(0.00, 6.91). Default: 100. Format: numeric. |

min_size | The initial cluster dedrogram is cut at an height such that the minimum cluster size is at least min_size; if min_size < 1 than the fraction of total samples is used, otherwise it is used as absoulte count. Domain: e^U(-6.91, 0.00). Default: 0.01. Format: numeric. |

min_feat | Minimum number of differentially expressed features between siblings. If this number is not reached, two neighboring clusters (siblings) in the pruned dendrogram get joined. Domain: U(1, 100). Default: 5. Format: integer. |

max_pval | Maximum P-value for differential expression computation. Domain: e^U(-16.12, 0.00). Default: 1e-04. Format: numeric. |

min_fc | Mimimum fold-change for differential expression computation. Domain: U(0, 5). Default: 2. Format: numeric. |

l | Neighborhood size. Domain: U(1, 50). Default: 10. Format: integer. |

A TI method wrapper to be used together with
`infer_trajectory`

Ellwanger, D.C., Scheibinger, M., Dumont, R.A., Barr-Gillespie, P.G., Heller, S., 2018. Transcriptional Dynamics of Hair-Bundle Morphogenesis Revealed with CellTrails. Cell Reports 23, 2901–2914.e14.