branchTest {monocle} | R Documentation

## Test for branch-dependent expression

### Description

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.

### Usage

    branchTest(
      cds,
      fullModelFormulaStr = "~sm.ns(Pseudotime, df = 3)*Branch",
      reducedModelFormulaStr = "~sm.ns(Pseudotime, df = 3)",
      branch_states = NULL,
      branch_point = 1,
      relative_expr = TRUE,
      cores = 1,
      branch_labels = NULL,
      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.
`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

### Value

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

[Package monocle version 2.22.0 Index]