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

Description Usage Arguments Value

View source: R/BEAM.R

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

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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

includeDescrip

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


Bioconductor-mirror/monocle documentation built on Aug. 10, 2017, 10:49 a.m.