Assigns genes to epochs

Assigns genes to epochs

assign_epochs(
  matrix,
  dynamic_object,
  method = "active_expression",
  p_value = 0.05,
  pThresh_DE = 0.05,
  active_thresh = 0.33,
  toScale = FALSE,
  forceGenes = TRUE
)

Arguments

matrix

genes-by-cells expression matrix

dynamic_object

individual path result of running define_epochs

method

method of assigning epoch genes, either "active_expression" (looks for active expression in epoch) or "DE" (looks for differentially expressed genes per epoch)

p_value

pval threshold if gene is dynamically expressed

pThresh_DE

pval if gene is differentially expressed. Ignored if method is active_expression.

active_thresh

value between 0 and 1. Percent threshold to define activity

toScale

whether or not to scale the data

forceGenes

whether or not to rescue orphan dyanmic genes, forcing assignment into epoch with max expression.

Value

epochs a list detailing genes active in each epoch