getUniverse {ramr} | R Documentation

## Merges, filters and outputs all genomic regions of a given 'GRanges' object

### Description

'getUniverse' returns a 'GRanges' object with all the genomic regions in a data set, that can be used for AMR enrichment analysis

### Usage

    getUniverse(data.ranges, merge.window = 300, min.cpgs = 7, min.width = 1)

### Arguments

`data.ranges` | A 'GRanges' object with genomic locations and corresponding beta values included as metadata.
`merge.window` | A single integer >= 1. All 'data.ranges' genomic locations within this distance will be merged (the default: 300).
`min.cpgs` | A single integer >= 1. All genomic regions containing less than 'min.cpgs' genomic locations are filtered out (the default: 7).
`min.width` | A single integer >= 1 (the default). Only regions with the width of at least 'min.width' are returned.

### Details

In the provided data set 'getUniverse' merges and outputs all the genomic regions that satisfy filtering criteria, thus creating a 'GRanges' object to be used as a reference set of genomic regions for AMR enrichment analysis.

### Value

The output is a 'GRanges' object that contain all the genomic regions in 'data.ranges' object (in other words, all potential AMRs).

### See Also

`getAMR` for identification of AMRs, `plotAMR` for plotting AMRs, `simulateAMR` and `simulateData` for the generation of simulated test data sets, and 'ramr' vignettes for the description of usage and sample data.

### Examples

      data(ramr)
      universe <- getUniverse(ramr.data, min.cpgs=5, merge.window=1000)

      # identify AMRs
      amrs <- getAMR(ramr.data, ramr.samples, ramr.method="beta", min.cpgs=5,
                     merge.window=1000, qval.cutoff=1e-3, cores=2)

      # AMR enrichment analysis using LOLA
      library(LOLA)
      # download LOLA region databases from http://databio.org/regiondb
      hg19.extdb.file <- system.file("LOLAExt", "hg19", package="LOLA")
      if (file.exists(hg19.extdb.file)) {
        hg19.extdb  <- loadRegionDB(hg19.extdb.file)
        runLOLA(amrs, universe, hg19.extdb, cores=1, redefineUserSets=TRUE)
      }

[Package ramr version 1.2.0 Index]