find_cuts_by_clustering: Returns cuts to define epochs

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

Description

Returns cuts to define epochs via clustering

Usage

find_cuts_by_clustering(
  expDat,
  dynRes,
  num_epochs,
  limit_to = NULL,
  method = "kmeans",
  pThresh_dyn = 0.05
)

Arguments

expDat	genes-by-cells expression matrix
dynRes	result of running findDynGenes or define_epochs
num_epochs	the number of epochs
limit_to	vector of genes on which to base epoch cuts, for example, limiting to TFs
method	what clustering method to use, either 'kmeans' or 'hierarchical'
pThresh_dyn	pval threshold if gene is dynamically expressed

Value

vector of pseudotimes at which to cut data into epochs

pcahan1/epoch documentation built on Feb. 14, 2022, 1:57 a.m.