define_epochs: Define epochs
In pcahan1/epoch: Dynamic GRN reconstruction from single cell RNA-Seq data

Define epochs

define_epochs(
  dynRes,
  expDat,
  method = "pseudotime",
  num_epochs = 2,
  pseudotime_cuts = NULL,
  group_assignments = NULL,
  pThresh_dyn = 0.05,
  winSize = 2
)

`dynRes`	results of running findDynGenes, or a list of results of running findDynGenes per path. If list, names should match names of expDat.
`expDat`	genes-by-cells expression matrix, or a list of expression matrices per path. If list, names should match names of dynRes.
`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