createMergedRepository {gep2pep}R Documentation

Merge multiple PEPs to build a repository of consensus PEPs

Description

Merge multiple PEPs to build a repository of consensus PEPs

Usage

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

Arguments

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.

Details

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.

Value

Nothing, used for side effects.

Examples


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)

[Package gep2pep version 1.2.0 Index]