nes_covariance: Compute the Covariance of the Directed and Undirected NES.

In califano-lab/PISCES: Protein Activity Inferecne in Single Cells

Compute the Covariance of the Directed and Undirected NES.

Description

Compute the Covariance of the Directed and Undirected NES.

Usage

nes_covariance(R, S, AW.AM.prod, AW.AM.abs.prod, E.r, E.rs, D.v, U.v, g)

Arguments

R	Rank normalized ges matrix (genes x samples).
S	Sign of ges matrix (genes x samples).
AW.AM.prod	Product of the association weight (AW) and mode (AM) matrices created from the regulon list.
AW.AM.abs.prod	Product of the association weight (AW) and absolute value of the association mode (AM.abs) matrices created from the regulon list.
E.r	Expected value of r in each sample (scalar value).
E.rs	Expected value of r*s in each sample (1 x samples).
D.v	Variance of Directed Enrichment Score (regulons x samples).
U.v	Variance of Undirected Enrichment Score (regulons x samples).
g	Number of genes in the gene expression signature matrix (scalar value).

Value

Matrix of covariance values (regulons x samples).

califano-lab/PISCES documentation built on Jan. 11, 2023, 5:34 a.m.