InferPotencyStates: Infer distinct potency states from the single cell potency...

In aet21/SCENT: Single Cell Entropy

Infer distinct potency states from the single cell potency estimates

Description

This function infers the discrete potency states of single cells and its distribution across the single cell population.

Usage

InferPotencyStates(
  potest.v,
  type = c("SR", "CCAT"),
  pheno.v = NULL,
  diffvar = TRUE,
  maxPS = 5
)

Arguments

potest.v	A vector of potency estimates for all cells, e.g. a vector of SR or CCAT values.
type	The type of potency estimate used (SR or CCAT).
pheno.v	A phenotype vector for the single cells.
diffvar	A logical. Default is TRUE. Specifies whether the Gaussian mixture model to be fit assumes components to have different (default) or equal variance. In the latter case, use *modelNames = c("E")*.
maxPS	Maximum number of potency states, when inferring discrete potency states of single cells. Default value is 5.

Value

A list with the following elements:

potS	Inferred discrete potency states for each single cell. It is indexed so that the index increases as the signaling entropy of the state decreases.
distr	If phenotype information provided, it will be a table giving the distribution of single-cells across potency states and phenotypes.
prob	Table giving the probabilities of each potency state per phenotype value.
het	The normalised Shannon Index of potency per phenotype value.

References

Teschendorff AE, Tariq Enver. Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome. Nature communications 8 (2017): 15599. doi: 10.1038/ncomms15599.

aet21/SCENT documentation built on Aug. 1, 2022, 12:05 p.m.