gene2pathways: Finds pathways including a given gene.
In gep2pep: Creation and Analysis of Pathway Expression Profiles (PEPs)

Description Usage Arguments Value See Also Examples

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.

1	gene2pathways(rp, genes, and = TRUE)

`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`.

A database of pathways suitable as input to PathSEA.

createRepository, PathSEA

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)