getRegionFile: Grab the filename for a a single region set from a database...

Description Usage Arguments Value Examples

View source: R/loadRegionDB.R

Description

Like getRegionSet but returns a filename instead of a GRanges object. Given a local filename, returns a complete absolulte path so you can read that file in.

Usage

1
getRegionFile(dbLocation, filenames, collections = NULL)

Arguments

dbLocation

folder of regionDB

filenames

Filename(s) of a particular region set to grab.

collections

(optional) subset of collections to list

Value

A filename the specified file in the regionDB.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
dbPath = system.file("extdata", "hg19", package="LOLA")
regionDB = loadRegionDB(dbLocation=dbPath)
data("sample_universe", package="LOLA")
data("sample_input", package="LOLA")

getRegionSet(regionDB, collections="ucsc_example", filenames="vistaEnhancers.bed")
getRegionSet(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed")
getRegionFile(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed")


res = runLOLA(userSets, userUniverse, regionDB, cores=1)
locResult = res[2,]
extractEnrichmentOverlaps(locResult, userSets, regionDB)
writeCombinedEnrichment(locResult, "temp_outfolder")

userSetsRedefined =	redefineUserSets(userSets, userUniverse)
resRedefined = runLOLA(userSetsRedefined, userUniverse, regionDB, cores=1)

g = plotTopLOLAEnrichments(resRedefined)

sheffien/LOLA documentation built on May 7, 2018, 12:58 a.m.