Define epochs
define_epochs_new(
dynamic_object,
matrix,
method = "pseudotime",
num_epochs = 2,
pseudotime_cuts = NULL,
group_assignments = NULL,
p_value = 0.05,
winSize = 2
)results of running findDynGenes, or a list of results of running findDynGenes per path. If list, names should match names of matrix.
genes-by-cells expression matrix, or a list of expression matrices per path. If list, names should match names of dynamic_object.
method to define epochs. Either "pseudotime", "cell_order", "group", "con_similarity", "kmeans", "hierarchical"
number of epochs to define. Ignored if epoch_transitions, pseudotime_cuts, or group_assignments are provided.
vector of pseudotime cutoffs. If NULL, cuts are set to max(pseudotime)/num_epochs.
a list of vectors where names(assignment) are epoch names, and vectors contain groups belonging to corresponding epoch
p_value
winSize
updated list of dynamic_object with epoch column included in dynamic_object$cells