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, gene)

Arguments

rp

A repository created by createRepository.

gene

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

Value

A database of pathways suitable as input to PathSEA.

See Also

createRepository, PathSEA

Examples

db <- loadSamplePWS()
db <- as.CategorizedCollection(db)
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 1.0.0 Index]