Define epochs

Define epochs

define_epochs(
  dynamic_object,
  matrix,
  method = "pseudotime",
  num_epochs = 2,
  pseudotime_cuts = NULL,
  group_assignments = NULL,
  p_value = 0.05,
  winSize = 2
)

Arguments

dynamic_object

results of running findDynGenes, or a list of results of running findDynGenes per path. If list, names should match names of matrix.

matrix

genes-by-cells expression matrix, or a list of expression matrices per path. If list, names should match names of dynamic_object.

method

method to define epochs. Either "pseudotime", "cell_order", "group", "con_similarity", "kmeans", "hierarchical"

num_epochs

number of epochs to define. Ignored if epoch_transitions, pseudotime_cuts, or group_assignments are provided.

pseudotime_cuts

vector of pseudotime cutoffs. If NULL, cuts are set to max(pseudotime)/num_epochs.

group_assignments

a list of vectors where names(assignment) are epoch names, and vectors contain groups belonging to corresponding epoch

p_value

p_value

winSize

winSize

Value

updated list of dynamic_object with epoch column included in dynamic_object$cells