gene2pathways {gep2pep}R Documentation

Finds pathways including a given gene.

Description

Given a gene, find the set of pathways that involve it in each collection of the repository. This can be used to define a set of pathways for the PathSEA.

Usage

gene2pathways(rp, genes, and = TRUE)

Arguments

rp

A repository created by createRepository.

genes

A vector of gene identifiers of the same type as that used to create the repository.

and

If set to TRUE (default), will return sets containing all of genes. Otherwise will return the sets containing any of genes.

Value

A database of pathways suitable as input to PathSEA.

See Also

createRepository, PathSEA

Examples

db <- loadSamplePWS()
repo_path <- file.path(tempdir(), "gep2pepTemp")

rp <- createRepository(repo_path, db)

## Finding all pathways containing "FAM126A":
subpw <- gene2pathways(rp, "FAM126A")

print(names(subpw))

unlink(repo_path, TRUE)


[Package gep2pep version 1.10.0 Index]