Description Usage Arguments Value

Testing for branch-dependent expression with `BEAM()`

first
involves constructing a CellDataSet that assigns each cell to a branch, and
then performing a likelihood ratio test to see if the branch assignments
significantly improves the fit over a null model that does not split the cells.
`branchTest()`

implements these two steps.

1 2 3 4 |

`cds` |
a CellDataSet object upon which to perform this operation |

`fullModelFormulaStr` |
a formula string specifying the full model in differential expression tests (i.e. likelihood ratio tests) for each gene/feature. |

`reducedModelFormulaStr` |
a formula string specifying the reduced model in differential expression tests (i.e. likelihood ratio tests) for each gene/feature. |

`branch_states` |
states corresponding to two branches |

`branch_point` |
The ID of the branch point to analyze. Can only be used when reduceDimension is called with method = "DDRTree". |

`relative_expr` |
a logic flag to determine whether or not the relative gene expression should be used |

`cores` |
the number of cores to be used while testing each gene for differential expression |

`branch_labels` |
the name for each branch, for example, AT1 or AT2 |

`verbose` |
Whether to show VGAM errors and warnings. Only valid for cores = 1. |

`...` |
Additional arguments passed to differentialGeneTest |

a data frame containing the p values and q-values from the likelihood ratio tests on the parallel arrays of models.

monocle documentation built on May 31, 2017, 11:12 a.m.

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