FindCorrelatedRegions {rnaEditr} | R Documentation

## Find contiguous co-edited subregions.

### Description

Find contiguous co-edited subregions based on the output file from function `MarkCoeditedSites`.

### Usage

    FindCorrelatedRegions(
      sites_df,
      featureType = c("site", "cpg"),
      minSites_int = 3
    )

### Arguments

`sites_df` | An output data frame from function `MarkCoeditedSites`, with variables `site, keep, ind, r_drop`. Please see `MarkCoeditedSites` for details.
`featureType` | Feature type, Defaults to `"site"`.
`minSites_int` | An integer indicates the minimum number of sites to be considered a contiguous co-edited region.

### Value

A data frame with the following columns:

- `site` : site ID.

- `subregion` : index for each output contiguous co-edited region.

### Examples

      data(t_rnaedit_df)

      ordered_cols <- OrderSitesByLocation(
        sites_char = colnames(t_rnaedit_df),
        output = "vector"
      )
      exm_data <- t_rnaedit_df[, ordered_cols]

      exm_sites <- MarkCoeditedSites(
        rnaEditCluster_mat = exm_data,
        method = "spearman"
      )

      FindCorrelatedRegions(
        sites_df = exm_sites,
        featureType = "site"
      )

[Package rnaEditr version 1.2.0 Index]