weights_from_pst: weights_from_pst

In HectorRDB/condiments: Differential Topology, Progression and Differentiation.

weights_from_pst

Description

Most trajectory inference methods do not perform soft assignment but instead assign cells to all possible lineages before a branching point, and then to one or another. This function re-creates a weight matrix from those matrices of pseudotime

Usage

weights_from_pst(pseudotime, ...)

## S4 method for signature 'matrix'
weights_from_pst(pseudotime)

## S4 method for signature 'data.frame'
weights_from_pst(pseudotime)

Arguments

pseudotime	A matrix or data.frame of \[ncells\] by \[nCurves\].
...	Other parameters including:

Value

A object of the same type and dimensions as the original object, with the weights for each curve and cell.

Examples

data(list = 'slingshotExample', package = "slingshot")
if (!"cl" %in% ls()) {
  rd <- slingshotExample$rd
  cl <- slingshotExample$cl
}
sds <- slingshot::slingshot(rd, cl)
weights_from_pst(slingshot::slingPseudotime(sds))

HectorRDB/condiments documentation built on Oct. 18, 2024, 10:13 p.m.