Description Usage Arguments Value Author(s) References Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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."
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 | # 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)
|
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