one_signature_activity: One signature activity

In greenelab/ADAGEpath: ADAGE-based Signature Analysis

One signature activity

Description

Calculates activities for a specific signature in an ADAGE model. If gene_set is provided, it will only calculate the acitivity of a signature using genes in the gene_set.

Usage

one_signature_activity(weight_matrix, express_matrix, node, side,
  gene_set = NULL, HW_cutoff = 2.5)

Arguments

weight_matrix	a data.matrix storing the weight matrix in an ADAGE model.
express_matrix	a data.matrix storing gene expression values in a dataset
node	an int ranging from 1 to number of columns in weight_matrix
side	character, "pos" or "neg"
gene_set	a character vector storing gene IDs, must match the gene IDs used in the model. (default: NULL)
HW_cutoff	number of standard deviations from mean in a node's weight distribution to be considered as high-weight (default to 2.5).

Value

a vector storing activities of one signature across samples

greenelab/ADAGEpath documentation built on May 25, 2022, 7:11 a.m.