signature_geneset_activity: Calculating gene set activity inside signatures

In greenelab/ADAGEpath: ADAGE-based Signature Analysis

Calculating gene set activity inside signatures

Description

Calculates activity of signatures only using genes in the provided gene sets

Usage

signature_geneset_activity(signature_geneset_df, gene_set_list, model,
  input_data, HW_cutoff = 2.5)

Arguments

signature_geneset_df	a data.frame with the first column specifying signature names and second column specifying gene set names.
gene_set_list	a named list storing all possible gene sets with each element being a vector of gene IDs. It is used to extract genes IDs given the name of a gene set.
model	the ADAGE model to be used for calculating signature activity.
input_data	a data.frame with gene IDs in the first column and expression values from the second column.
HW_cutoff	number of standard deviations away from mean in a node's weight distribution to be considered as high-weight (default to 2.5).

Value

a data.frame with the first column being "signature|geneset" names and the rest columns storing activities for every sample in the input_data.

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