createMergedRepository: Merge multiple PEPs to build a repository of consensus PEPs
In gep2pep: Creation and Analysis of Pathway Expression Profiles (PEPs)

Description Usage Arguments Details Value Examples

Merge multiple PEPs to build a repository of consensus PEPs

1 2	createMergedRepository(rpIn_path, rpOut_path, mergestr, progressBar = TRUE, collections = "all")

`rpIn_path`	path to existing gep2pep repository
`rpOut_path`	path where the new merged repository will be created
`mergestr`	a named list of character vectors, each one including a set of PEP names. For each list entry, a consensus PEP will be created and assigned the entry name.
`progressBar`	if TRUE, show a progress bar
`collections`	A subset of the collection names returned by `getCollections`. If set to "all" (default), all the collections in `rp` will be used.

The merging is performed as follows. Given N PEPs, the corresponding consensus PEP will get as enrichement score the average enrichment scores of the N PEPs, and as p-value the composition of the N PEP p-values by Fisher's method.

Nothing, used for side effects.

db <- loadSamplePWS()
repo_path <- file.path(tempdir(), "gep2pepTemp")
rp <- createRepository(repo_path, db)
geps <- loadSampleGEP()
buildPEPs(rp, geps)

mergestr <- list(
    che_iso = c("(+)_chelidonine", "(+)_isoprenaline"),
    cat_mk = c("(+/_)_catechin", "(_)_mk_801")
)

merged_path <- file.path(tempdir(), "gep2pepTempMerged")

createMergedRepository(repo_path, merged_path, mergestr)

unlink(repo_path, TRUE)
unlink(merged_path, TRUE)