pcxn_explore_analyze {pcxn} | R Documentation |
Using pcxn_explore, select a single pathway/gene set from one of the four collections ( MSigDB H hallmark gene sets, MSigDB C2 Canonical pathways, MSigDB C5 GO BP gene sets, and Pathprint ) and discover its correlated pathway/gene sets within the same collection.
Using pcxn_analyze, discover correlation relationships among multiple pathways/gene sets identified by GSEA (gene set enrichment analysis). All the input pathways/gene sets should come from the same collection. MSigDB H hallmark gene sets, MSigDB C2 Canonical pathways, MSigDB C5 GO BP gene sets, and Pathprint are treated as four separate collections.
pcxn_explore(collection = c("pathprint", "MSigDB_H","MSigDB_C2_CP", "MSigDB_C5_GO_BP"), query_geneset, adj_overlap = FALSE, top = 10, min_abs_corr = 0.05, max_pval = 0.05) pcxn_analyze(collection = c("pathprint", "MSigDB_H","MSigDB_C2_CP", "MSigDB_C5_GO_BP"), phenotype_0_genesets, phenotype_1_genesets, adj_overlap = FALSE, top = 10, min_abs_corr = 0.05, max_pval = 0.05)
collection |
pathways' collection chosen among: "pathprint", "MSigDB_H", "MSigDB_C2_CP", "MSigDB_C5_GO_BP" |
query_geneset |
the single pathway of interest |
phenotype_0_genesets |
genesets/pathways of the first group of pathways |
phenotype_1_genesets |
genesets/pathways of the second group of pathways |
adj_overlap |
whether the correlation coefficients are adjusted for gene overlap |
top |
most correlated genesets/pathways |
min_abs_corr |
minimum absolute correlation |
max_pval |
maximum p-value |
a pcxn object
Sokratis Kariotis
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."
# pcxn_explore function can be used with the default parameters: pcxn_explore("pathprint","Alzheimer's disease (KEGG)") # If specific parameters are desired we can use the full list of arguments: pcxn_explore("pathprint","Alzheimer's disease (KEGG)", FALSE, 100, 0.02, 0.045) # pcxn_analyze can be used with two gene sets and the default parameters: pcxn_analyze("pathprint",c("ABC transporters (KEGG)", "ACE Inhibitor Pathway (Wikipathways)", "AR down reg. targets (Netpath)"), c("DNA Repair (Reactome)")) # Alternatively, you can use only one gene set: pcxn_analyze("MSigDB_H",c("HALLMARK_COAGULATION","HALLMARK_UV_RESPONSE_UP")) # If specific parameters are desired we can use the full list of arguments: pcxn_analyze("pathprint",c("ABC transporters (KEGG)", "ACE Inhibitor Pathway (Wikipathways)", "AR down reg. targets (Netpath)"), c("DNA Repair (Reactome)"), FALSE, top = 100, min_abs_corr = 0.025, max_pval = 0.03)