Description Usage Arguments Details Value Examples

View source: R/FateID_functions.R

This function computes a principal curve for a given dimensional reduction representation which is specified by component names of an object returned by `compdr`

using the princurve package.

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`y` |
clustering partition. A vector with an integer cluster number for each cell. The order of the cells has to be the same as for the columns of x. |

`fb` |
fateBias object returned by the function |

`dr` |
list of dimensional reduction representations returned by the function |

`k` |
integer number for the dimension to be used. This dimension has to be present in |

`m` |
name of the dimensional reduction algorithms to be used for the principal curve computation. One of |

`trthr` |
real value representing the threshold of the fraction of random forest votes required for the inclusion of a given cell for the computation of the principal curve. If |

`start` |
integer number representing a specified starting cluster number for all trajectories, i. e. a common progenitor cluster. The argument is optional. Default value is |

`...` |
additional arguments to be passed to the low level function |

The function computes a principal curve for each differentiation trajectory by considering only cells that are assigned to the trajectory with a significant fate bias >1 or at least `trthr`

of the random forest votes, respectively.

For simulateneous computation and plotting of the principal curve, see function `plotFateMap`

.

A list of the following two components:

`pr` |
A list of principal curve objects produced by the |

`trc` |
A list of ordered cell IDs for each trajectory in |

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