View source: R/InferPotencyStates.R

InferPotencyStates | R Documentation |

This function infers the discrete potency states of single cells and its distribution across the single cell population.

InferPotencyStates( potest.v, type = c("SR", "CCAT"), pheno.v = NULL, diffvar = TRUE, maxPS = 5 )

`potest.v` |
A vector of potency estimates for all cells, e.g. a vector of SR or CCAT values. |

`type` |
The type of potency estimate used (SR or CCAT). |

`pheno.v` |
A phenotype vector for the single cells. |

`diffvar` |
A logical. Default is TRUE. Specifies whether the Gaussian mixture model to be fit assumes components to have different (default) or equal variance. In the latter case, use *modelNames = c("E")*. |

`maxPS` |
Maximum number of potency states, when inferring discrete potency states of single cells. Default value is 5. |

A list with the following elements:

`potS` |
Inferred discrete potency states for each single cell. It is indexed so that the index increases as the signaling entropy of the state decreases. |

`distr` |
If phenotype information provided, it will be a table giving the distribution of single-cells across potency states and phenotypes. |

`prob` |
Table giving the probabilities of each potency state per phenotype value. |

`het` |
The normalised Shannon Index of potency per phenotype value. |

Teschendorff AE, Tariq Enver.
*Single-cell entropy for accurate estimation of differentiation
potency from a cellâ€™s transcriptome.*
Nature communications 8 (2017): 15599.
doi:
10.1038/ncomms15599.

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