pcxn.db-package: Pathway correlation coefficients and p values between...

In hidelab/pcxn.db: Pathway correlation coefficients and p values between pre-defined gene sets

Description

PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively

Details

Package:	pcxn.db
Type:	Package
Version:	1.0.0
Date:	2017-08-20
License:	GPL

Author(s)

Sokratis Kariotis
Maintainer: Sokratis Kariotis [e-mail]

References

Pita-Juarez Y.,Altschuler G.,Kariotis S.,Wei W.,Koler K.,Tanzi R. and W. A. Hide (2017). "The Pathway Coexpression Network: Revealing Pathway Relationships."

Examples

require(pheatmap)
library(pcxn.db)
# load  the data
ds = c("cp_gs_v5.1", "gobp_gs_v5.1", "h_gs_v5.1","pathprint.Hs.gs",
  "pathCor_CPv5.1_dframe","pathCor_GOBPv5.1_dframe","pathCor_Hv5.1_dframe",
  "pathCor_pathprint_v1.2.3_dframe")
data(list = ds)

# Explore the static extendable network by focusing on single pathways and their
# 10 most correlated neighbours in the pathprint collection
pcxn_obj <- explore_pcxn(collection = "pathprint",
                  query_geneset = "Alzheimer's disease (KEGG)", 
                  top = 10, 
                  min_abs_corr = 0.05, 
                  max_pval = 0.05)

# Analyse relationships between groups of pathways shown to be enriched in the 
# collection by gene set enrichment 
pcxn_obj <- analyze_pcxn(collection = "pathprint",
            phenotype_0_genesets = c("ABC transporters (KEGG)",
                                     "ACE Inhibitor Pathway (Wikipathways)",
                                     "AR down reg. targets (Netpath)"),
            phenotype_1_genesets = c("DNA Repair (Reactome)"), 
            top = 10, 
            min_abs_corr = 0.05, 
            max_pval = 0.05 )

# Generate the heatmap for any pcxn object generated by the 
# explore or analyze function
hm <- heatmap_pcxn(pcxn_obj , cluster_method = "complete")

# Get the gene members (Entrez Ids and names) of any pathway/geneset in the 
# data
genesets_list <- gmembers_pcxn(pathway_name = "Alzheimer's disease (KEGG)")

# Create a network for any pcxn object generated by the 
# explore or analyze function
network <- network_pcxn(pcxn_obj)

hidelab/pcxn.db documentation built on May 30, 2019, 8:04 p.m.