differentialGeneTest {monocle} | R Documentation

## Test genes for differential expression

### Description

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.

### Usage

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

### Arguments

`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.

### Value

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

### See Also

`vglm`

[Package monocle version 2.15.0 Index]