dpt

Compute Diffusion Pseudotime from Transition Matrix (Eigen Decomposition)

Usage

dpt(T_mat, root, k = 30)

Arguments

T_mat

A square transition matrix (e.g., from kNN graph).

root

Integer. Index of the root cell.

k

Integer. Number of eigenvectors to use (default: 30).

Value

A numeric vector of pseudotime values normalized to [0, 1].

Details

Calculates pseudotime by spectral decomposition of a diffusion transition matrix, using a root cell as a reference point in the reduced diffusion space.

Examples

T <- matrix(runif(100), 10, 10)
T <- T / rowSums(T)
pt <- dpt(T, root = 1)
#> Error in dpt(T, root = 1): could not find function "dpt"