Description Usage Arguments Value See Also

View source: R/differential_expression.R

Tests each gene for differential expression as a function of pseudotime
or according to other covariates as specified. `differentialGeneTest`

is
Monocle's main differential analysis routine.
It accepts a CellDataSet and two model formulae as input, which specify generalized
lineage models as implemented by the `VGAM`

package.

1 2 3 | ```
differentialGeneTest(cds, fullModelFormulaStr = "~sm.ns(Pseudotime, df=3)",
reducedModelFormulaStr = "~1", relative_expr = TRUE, cores = 1,
verbose = FALSE)
``` |

`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. |

`relative_expr` |
Whether to transform expression into relative values. |

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

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

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

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