View source: R/tree-structure.R
All Segment Divergence By Pseudotime
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | allSegmentDivergenceByPseudotime(
object,
pseudotime,
segments,
divergence.method = c("ks", "preference"),
pseudotime.cuts = 80,
window.size = 5,
minimum.visits = 10,
visit.threshold = 0.7,
p.thresh = 0.01,
pref.thresh = 0.5,
breakpoint.decision.plots = NULL,
cache = T,
verbose = F
)
|
object |
An URD object |
pseudotime |
(Character) Name of pseudotime to use for determining pseudotime of breakpoints |
segments |
(Character vector) Segments to consider fot determining visit divergence |
divergence.method |
(Character: "ks" or "preference") Test to use to determine whether visitation has diverged for each pseudotime window. |
pseudotime.cuts |
(Numeric) Approximate number of cells to assign to each pseudotime bin for branchpoint finding. |
window.size |
(Numeric) Width of moving window in pseudotime used for branchpoint finding, in terms of bins. |
minimum.visits |
(Numeric) Minimum number of random walk visits to a cell to retain it in the tree |
visit.threshold |
(Numeric) Cells are considered potential members for segments/tips from which random walks visited them at least this fraction of their maximum visitation from a single tip |
p.thresh |
(Numeric) p-value threshold to use in determining whether visitation is significantly different from pairs of tips |
pref.thresh |
(Numeric) Maximum mean preference within a window to be considered 'different' if |
breakpoint.decision.plots |
(Path) Path to save plots summarizing (default is NULL, which does not save plots as they are somewhat slow) |
cache |
(Logical) Used cached values? This will check |
verbose |
(Logical) Report on progress? |
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