GetPathFun: Enriched biological pathways

In bozdaglab/CTDPathSim2.0: Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

Enriched biological pathways

Description

This function identifies the enriched biological pathways for each sample and cell line utilizing the DE genes. It finds enriched biological pathways listed in the REACTOME database via a pathway enrichment tool Pathfinder. To prioritize cancer-related biological pathways, specifically, it uses the known frequently mutated genes that were considered cancer-driving genes from the DE gene list for this analysis. We obtained the frequently mutated cancer-driving genes from the COSMIC database. GetPath() considers the pathways that were significantly enriched with FDR-corrected hypergeometric p-values < 0.05 in this DE cancer gene list.

Usage

GetPathFun(CancerGeneList, SampleCell_de_genes)

Arguments

CancerGeneList	A R dataframe with a column of frequently mutated cancer driver genes.
SampleCell_de_genes	A R dataframe with a column containing DE genes of a sample or cell line.

Details

Created By: Banabithi Bose| Date Created: 4/10/2022 | Stage 3 | Function 3 |

Value

An R dataframe object with three columns labeled as 'ID', 'reactome_pathway', and 'p.adjust.pat', respectively.

bozdaglab/CTDPathSim2.0 documentation built on April 14, 2022, 12:39 a.m.