find_associated_signatures: Associated signatures retrieval

In greenelab/ADAGEpath: ADAGE-based Signature Analysis

Associated signatures retrieval

Description

Returns the significantly associated signatures for the input genesets. If signature_limma_result is provided, it will only return the significantly associated signatures that achieves the lowest adjusted p-value in the signature_limma_result.

Usage

find_associated_signatures(input_genesets, gene_set_list, model,
  significance_cutoff = 0.05, signature_limma_result = NULL)

Arguments

input_genesets	a character vector storing gene set names, must be found in the provided gene set list
gene_set_list	a named list storing all possible gene sets with each element being a vector of gene IDs.
model	an ADAGE model to extract signatures from
significance_cutoff	numeric, FDR significance cutoff used to determine signature-geneset association (default: 0.05).
signature_limma_result	a data.frame that stores the result table returned by limma. It includes logFC, adj.P.Val, and other statistics for each signature.

Value

a list storing associated signatures for each input gene set

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