AllCloseByRegions {rnaEditr} | R Documentation

## Extract clusters of RNA editing sites located closely in genomic regions.

### Description

A wrapper function to extract clusters of RNA editing sites that are located closely in genomic regions.

### Usage

    AllCloseByRegions(
      regions_gr,
      rnaEditMatrix,
      maxGap = 50,
      minSites = 3,
      progressBar = "time"
    )

### Arguments

`regions_gr` | A GRanges object of input genomic regions.
`rnaEditMatrix` | A matrix (or data frame) of RNA editing level values on individual sites, with row names as site IDs in the form of "chrAA:XXXXXXXX", and column names as sample IDs. Please make sure to follow the format of example dataset (`data(rnaedit_df)`).
`maxGap` | An integer, genomic locations within `maxGap` from each other are placed into the same cluster. Defaults to 50.
`minSites` | An integer, minimum number of RNA editing sites within each resulting cluster. Defaults to 3.
`progressBar` | Name of the progress bar to use. There are currently five types of progress bars: `"time"`, `"none"`, `"text"`, `"tk"`, and `"win"`. Defaults to `"time"`. See `create_progress_bar` for more details.

### Details

The algorithm of this function is based on the `clusterMaker` function in the `bumphunter` R package. Each cluster is essentially a group of site locations such that two consecutive locations in the cluster are separated by less than `maxGap`.

### Value

A GRanges object containing genomic regions of RNA editing sites located closely within each input pre-defined genomic region.

### See Also

`TransformToGR`, `AllCoeditedRegions`, `CreateEditingTable`, `SummarizeAllRegions`, `TestAssociations`, `AnnotateResults`

### Examples

      data(rnaedit_df)

      exm_regions <- TransformToGR(
        genes_char = c("PHACTR4", "CCR5", "METTL7A"),
        type = "symbol",
        genome = "hg19"
      )

      AllCloseByRegions(
        regions_gr = exm_regions,
        rnaEditMatrix = rnaedit_df,
        maxGap = 50,
        minSites = 3,
        progressBar = "time"
      )

[Package rnaEditr version 1.4.0 Index]