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

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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.

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