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Canonical Redundancy Analysis for Tocky Differentiation using single-cell RNA-sequencing data (CanonicalTockySeq)

Source: R/CanonicalTockySeq.R
CanonicalTockySeq.Rd

Performs a specialized Canonical Redundancy Analysis (RDA) designed for single-cell Tocky data. In this architecture, genes are treated as "sites" and cells as "species", constrained by Tocky-defined developmental stages (Blue, Blue-Red, Red).

Usage

CanonicalTockySeq(X, Z)

Arguments

X

Numeric matrix of gene expression (Genes x Cells).

Z

Numeric matrix of explanatory variables (Genes x Signatures). Typically contains Tocky-specific gene signatures (e.g., Blue, Blue-Red, Red).

Value

A list containing:

expression_scores

Data frame of Gene loadings (Genes x k).

fitted_cell_scores

Data frame of Fitted Cell scores (Cells x k).

cell_scores

Data frame of Cell scores (Cells x k). Use this for downstream GradientTockySeq.

biplot

Matrix of biplot vectors for the constraint variables (Z).

Details

Implements the two-step RDA procedure described by Legendre & Legendre (2012):

  1. Multivariate regression of Expression (X) on Constraints (Z).

  2. PCA of the fitted values to derive canonical axes.