analyze_pcxn: Discover correlation relationships among multiple...

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

Description

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.

Usage

analyze_pcxn(collection = "pathprint",
  phenotype_0_genesets = c("ABC transporters (KEGG)",
  "ACE Inhibitor Pathway (Wikipathways)", "AR down reg. targets (Netpath)"),
  phenotype_1_genesets = c(), top = 10, min_abs_corr = 0.05,
  max_pval = 0.05)

Arguments

collection	pathway's collection
phenotype_0_genesets	genesets/pathways of the first group of pathways
phenotype_1_genesets	genesets/pathways of the second group of pathways
top	most correlated genesets/pathways
min_abs_corr	minimum absolute correlation
max_pval	maximum p-value

Value

pcxn object

Examples

## Not run: 
 analyze_pcxn("pathprint",c("ABC transporters (KEGG)",
 "ACE Inhibitor Pathway (Wikipathways)","AR down reg. targets (Netpath)"),
  c("DNA Repair (Reactome)"), 10, 0.05, 0.05)

## End(Not run)

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