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

`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.

Value

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

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.

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)
# \donttest{
  # identify AMRs
  amrs <- getAMR(ramr.data, ramr.samples, ramr.method="beta", min.cpgs=5,
                 merge.window=1000, qval.cutoff=1e-3, cores=2)
#> Identifying AMRs
#>  [4.299s]

  # 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)
  }
# }