detectBifurcationPoint: Calculate divergence times for branch-dependent genes

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

Description

Branch-dependent genes may diverge at different points in pseudotime. detectBifurcationPoint() calculates these times. Although the branch times will be shaped by and distributed around the branch point in the trajectory, upstream regulators tend to branch earlier in pseudotime than their targets.

Usage

detectBifurcationPoint(str_log_df = NULL, ILRs_threshold = 0.1,
  detect_all = T, cds = cds, Branch = "Branch", branch_point = NULL,
  branch_states = c(2, 3), stretch = T, cores = 1,
  trend_formula = "~sm.ns(Pseudotime, df = 3)", ILRs_limit = 3,
  relative_expr = TRUE, label_by_short_name = TRUE, useVST = FALSE,
  round_exprs = FALSE, output_type = "all", return_cross_point = T,
  file = "bifurcation_heatmap", verbose = FALSE, ...)

Arguments

str_log_df	the ILRs dataframe calculated from calILRs function. If this data.frame is provided, all the following parameters are ignored. Note that we need to only use the ILRs after the bifurcation point if we duplicated the progenitor cell state.
ILRs_threshold	the ILR value used to determine the earliest divergence time point
detect_all	a logic flag to determine whether or not genes without ILRs pass the threshold will still report a bifurcation point
cds	CellDataSet for the experiment
Branch	The column in pData used for calculating the ILRs (If not equal to "Branch", a warning will report)
branch_point	The ID of the branch point to analyze. Can only be used when reduceDimension is called with method = "DDRTree".
branch_states	The states for two branching branchs
stretch	a logic flag to determine whether or not each branch should be stretched
cores	Number of cores when fitting the spline curves
trend_formula	the model formula to be used for fitting the expression trend over pseudotime
ILRs_limit	the minimum Instant Log Ratio used to make the heatmap plot
relative_expr	A logic flag to determine whether or not the relative expressed should be used when we fitting the spline curves
label_by_short_name	label the rows of the returned matrix by gene_short_name (TRUE) or feature id (FALSE)
useVST	A logic flag to determine whether or not the Variance Stablization Transformation should be used to stablize the gene expression. When VST is used, the difference between two branchs are used instead of the log-ratio.
round_exprs	A logic flag to determine whether or not the expression value should be rounded into integer
output_type	A character either of "all" or "after_bifurcation". If "after_bifurcation" is used, only the time points after the bifurcation point will be selected. Note that, if Branch is set to "Branch", we will only use "after_bifurcation" since we duplicated the progenitor cells and the bifurcation should only happen after the largest mature level from the progenitor cells
return_cross_point	A logic flag to determine whether or not only return the cross point
file	the name for storing the data. Since the calculation of the Instant Log Ratio is very time consuming, so by default the result will be stored
verbose	Whether to report verbose output
...	Additional arguments passed to calILRs

Value

a vector containing the time for the bifurcation point with gene names for each value

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