createMergedRepository {gep2pep} | R Documentation |
Merge multiple PEPs to build a repository of consensus PEPs
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
|
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)