getEntropy: calculate scEntropies of individual cells

In minzheguo/SLICE: Determining Cell Differentiation and Lineage based on Single Cell Entropy

calculate scEntropies of individual cells

Description

performing bootstrap or deterministic calculation of scEntropy

Usage

getEntropy(
  object,
  clusters = NULL,
  km = NULL,
  calculation = "bootstrap",
  exp.cutoff = 1,
  B.size = 1000,
  B.num = 1,
  clustering.k = 0,
  random.seed = 201602,
  ...
)

Arguments

object	Slice object
km	A symmetric matrix encoding the functional similarity of genes; the row names and column names must be official NCBI gene symbols.
calculation	Choose the "bootstrap" or "deterministic" calculation of scEntropy
exp.cutoff	The expression threshold of a gene to be considered expressed
B.size	In bootstrap calculation, specifies the size of bootstrap sample; in deterministic calculation, specific the number of top expressed genes from each cell
B.num	The number of bootstrap samples
clustering.k	The number of functional clusters
random.seed	The seed for randomness
cluster	A data frame containing the functional clustering of genes; contains two columns "GENE" - official NCBI gene symbols and "CLUSTER" - cluster memberships.

Value

an slice object with calculated entropies in the "entropy" and "entropies" slots

minzheguo/SLICE documentation built on June 5, 2023, 11:56 a.m.