explore_pcxn: Select a single pathway/gene set from one of the four...

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

Description

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.

Usage

explore_pcxn(collection = "pathprint",
  query_geneset = "Alzheimer's disease (KEGG)", top = 10,
  min_abs_corr = 0.05, max_pval = 0.05)

Arguments

collection	pathways' collection
query_geneset	the single pathway of interest
top	most correlated genesets/pathways
min_abs_corr	minimum absolute correlation
max_pval	maximum p-value

Value

pcxn object

Examples

## Not run: 
 explore_pcxn("pathprint","Alzheimer's disease (KEGG)", 10,
 0.05, 0.05)

## End(Not run)

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