Description Details Author(s) References Examples
Discover the correlated pathways/gene sets of a single pathway/gene set or discover correlation relationships among multiple pathways/gene sets. Draw a heatmap or create a network of your query and extract members of each pathway/gene set found in the available collections (MSigDB H hallmark, MSigDB C2 Canonical pathways, MSigDB C5 GO BP and Pathprint).
Package: | pcxn |
Type: | Package |
Version: | 2.0.0 |
Date: | 2018-4-1 |
License: | MIT |
Sokratis Kariotis, Yered Pita-Juarez, Winston Hide, Wenbin Wei
Maintainer: Sokratis Kariotis s.kariotis@sheffield.ac.uk
Pita-Juarez Y.,Altschuler G.,Kariotis S.,Wei W.,Koler K.,Tanzi R. and W. A. Hide (2018). "The Pathway Coexpression Network: Revealing Pathway Relationships."
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | library(pcxnData)
# 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_CPv5.1_unadjusted_dframe",
"pathCor_GOBPv5.1_dframe",
"pathCor_GOBPv5.1_unadjusted_dframe",
"pathCor_Hv5.1_dframe",
"pathCor_Hv5.1_unadjusted_dframe",
"pathCor_pathprint_v1.2.3_dframe",
"pathCor_pathprint_v1.2.3_unadjusted_dframe")
data(list = ds)
# Explore the static extendable network (correlation coefficients are adjusted
# for gene overlap) by focusing on single pathways and their 10 most correlated
# neighbours in the pathprint collection
pcxn.obj <- pcxn_explore(collection = "pathprint",
query_geneset = "Alzheimer's disease (KEGG)",
adj_overlap = TRUE,
top = 10,
min_abs_corr = 0.05,
max_pval = 0.05)
# Explore the static extendable network (correlation coefficients are not
# adjusted for gene overlap) by focusing on single pathways and their
# 10 most correlated neighbours in the pathprint collection
pcxn.obj <- pcxn_explore(collection = "pathprint",
query_geneset = "Alzheimer's disease (KEGG)",
adj_overlap = FALSE,
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 (correlation coefficients are adjusted
# for gene overlap)
pcxn.obj <- pcxn_analyze(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)"),
adj_overlap = TRUE,
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 (correlation coefficients are not adjusted
# for gene overlap)
pcxn.obj <- pcxn_analyze(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)"),
adj_overlap = FALSE,
top = 10,
min_abs_corr = 0.05,
max_pval = 0.05 )
# Generate the heatmap for any pcxn object generated by the pcxn_explore() or
# pcxn_analyze() function
hm <- pcxn_heatmap(pcxn.obj , cluster_method = "complete")
# Get the gene members (Entrez Ids and names) of any pathway/geneset in the
# available collections
genesets_list <- pcxn_gene_members(pathway_name = "Alzheimer's disease (KEGG)")
# Create a network for any pcxn object generated by the pcxn_explore() or
# pcxn_analyze() function
# network <- pcxn_network(pcxn.obj)
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