calABCs: Compute the area between curves (ABC) for branch-dependent...

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

Description

This function is used to calculate the ABC score based on the the nature spline curves fitted for each branch. ABC score is used to quantify the total magnitude of divergence between two branchs. By default, the ABC score is the area between two fitted spline curves. The ABC score can be used to rank gene divergence. When coupled with p-val calculated from the branchTest, it can be used to identify potential major regulators for branch bifurcation.

Usage

calABCs(cds, trend_formula = "~sm.ns(Pseudotime, df = 3)*Branch",
  branch_point = 1, trajectory_states = NULL, relative_expr = TRUE,
  stretch = TRUE, cores = 1, verbose = F, min_expr = 0.5,
  integer_expression = FALSE, num = 5000, branch_labels = NULL, ...)

Arguments

cds	a CellDataSet object upon which to perform this operation
trend_formula	a formula string specifying the full model in differential expression tests (i.e. likelihood ratio tests) for each gene/feature.
branch_point	the point where two branches diverge
trajectory_states	States corresponding to two branches
relative_expr	a logic flag to determine whether or not the relative gene expression should be used
stretch	a logic flag to determine whether or not each branch should be stretched
cores	the number of cores to be used while testing each gene for differential expression
verbose	a logic flag to determine whether or not we should output detailed running information
min_expr	the lower limit for the expressed gene
integer_expression	the logic flag to determine whether or not the integer numbers are used for calculating the ABCs. Default is False.
num	number of points on the fitted branch trajectories used for calculating the ABCs. Default is 5000.
branch_labels	the name for each branch, for example, AT1 or AT2
...	Additional arguments passed to buildBranchCellDataSet

Value

a data frame containing the ABCs (Area under curves) score as the first column and other meta information from fData

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