Compute geneset expression as the average log-ration of genes in the geneset. Requires log-expression matrix X and (sparse) geneset matrix matG.

Compute geneset expression as the average log-ration of genes in the geneset. Requires log-expression matrix X and (sparse) geneset matrix matG.

Usage

gset_averageCLR(X, matG, center = TRUE)

Arguments

X

Log-expression matrix with genes on rows and samples on columns

matG

Sparse gene set matrix with genes on rows and gene sets on columns

center

Logical indicating whether to center the results

use.rank

Logical indicating whether to use rank transformation

Value

Matrix of gene set expression scores with gene sets on rows and samples on columns.