analyze_pcxn: Discover correlation relationships among multiple...

Description Usage Arguments Value Examples

View source: R/analyze_pcxn.R

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

1
2
3
4
5
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

1
2
3
4
5
6
## 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 Sept. 7, 2017, 7:19 p.m.