buildBranchCellDataSet {monocle} | R Documentation

## Build a CellDataSet that splits cells among two branches

### Description

Analyzing branches with `BEAM()` requires fitting two models to the expression data for each gene. The full model assigns each cell to one of the two outcomes of the branch, and the reduced model excludes this assignment. `buildBranchBranchCellDataSet()` takes a CellDataSet object and returns a version where the cells are assigned to one of two branches. The branch for each cell is encoded in a new column, "Branch", in the pData table in the returned CellDataSet.

### Usage

    buildBranchCellDataSet(cds, progenitor_method = c("sequential_split",
      "duplicate"), branch_states = NULL, branch_point = 1,
      branch_labels = NULL, stretch = TRUE)

### Arguments

`cds` | CellDataSet for the experiment
`progenitor_method` | The method to use for dealing with the cells prior to the branch
`branch_states` | The states for two branching branches
`branch_point` | The ID of the branch point to analyze. Can only be used when `reduceDimension()` is called with `reduction_method = "DDRTree"`.
`branch_labels` | The names for each branching branch
`stretch` | A logical flag to determine whether or not the pseudotime trajectory for each branch should be stretched to the same range or not

### Value

a CellDataSet with the duplicated cells and stretched branches

[Package monocle version 2.12.0 Index]