buildBranchCellDataSet: Build a CellDataSet that splits cells among two branches

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

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

monocle documentation built on Nov. 8, 2020, 5:06 p.m.