SingleCloseByRegion {rnaEditr} | R Documentation

## Extracts clusters of RNA editing sites located closely in a single genomic region.

### Description

Extracts clusters of RNA editing sites located closely in an input genomic region.

### Usage

    SingleCloseByRegion(region_df, rnaEditMatrix, maxGap = 50, minSites = 3)

### Arguments

`region_df` | A data frame with the input genomic region. Please make sure columns `seqnames`, `start`, and `end` are included in the data frame.
`rnaEditMatrix` | A matrix (or data frame) of RNA editing level values for 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 edited sites for a cluster to be selected for output. Defaults to 3.

### Details

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

### Value

A GRanges object containing genomic locations of RNA editing sites located closely within the single input pre-defined genomic region.

### Examples

      data(rnaedit_df)

      exm_region <- data.frame(
        seqnames = "chr1",
        start =  28691093,
        end = 28826881,
        stringsAsFactors = FALSE
      )

      SingleCloseByRegion(
        region_df = exm_region,
        rnaEditMatrix = rnaedit_df,
        maxGap = 50,
        minSites = 3
      )

[Package rnaEditr version 1.4.0 Index]