Fast Get LMDS

Fast Get LMDS

fast_get_lmds(
  W,
  max_time = 2^15,
  init_state,
  P_ls = NULL,
  correction = FALSE,
  largeData = TRUE,
  highres = FALSE
)

Arguments

W

matrix; the affinity matrix.

max_time

integer; the maximum diffusion time. Default is 2^15. The actual maximum diffusion time may be shorter if all nodes converge beforehand.

init_state

matrix; the row-wise normalized expression matrix.

P_ls

list; the list of diffusion operators. Default is NULL.

correction

logical; if TRUE, adjusts the score profile by scaling the score profile by entropy and applying delta correction. Default is FALSE.

largeData

logical; if TRUE, uses fast_calculate_score_profile_largeData. Default is TRUE.

highres

logical; if TRUE, uses fast_calculate_score_profile_highres. Default is FALSE.

Value

A list containing:

score_profile

data frame; the computed score profile for different diffusion times.

cumulative_score

numeric vector; the LMDS for each row in the score profile.