SitesToRegion {rnaEditr} | R Documentation

## Create output data in the format of GRanges.

### Description

Output contiguous co-edited subregions found by `FindCorrelatedRegions` function and filtered by `GetMinPairwiseCor` function.

### Usage

    SitesToRegion(
      sitesSubregion_df,
      sitesAreOrdered = TRUE,
      keepminPairwiseCor_df,
      returnAllSites = FALSE,
      verbose = TRUE
    )

### Arguments

`sitesSubregion_df` | An output data frame from function `FindCorrelatedRegions` with variables `site, subregion`. Please see `FindCorrelatedRegions` for details.
`sitesAreOrdered` | Are the sites in `sitesSubregion_df` ordered by location? Defaults to FALSE.
`keepminPairwiseCor_df` | An output data frame from function `GetMinPairwiseCor` with variables `subregion`, `keepminPairwiseCor` and `minPairwiseCor`. Please see `GetMinPairwiseCor` for details.
`returnAllSites` | When no contiguous co-edited regions are found in a input genomic region, `returnAllSites = TRUE` indicates outputting all the sites in this input region, while `returnAllSites = FALSE` indicates not returning any site in this input region. Defaults to FALSE.
`verbose` | Should messages and warnings be displayed? Defaults to TRUE.

### Value

A GRanges object with `seqnames`, `ranges` and `strand` of the contiguous co-edited regions.

### 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"
      )

      exm_regions <- FindCorrelatedRegions(
        sites_df = exm_sites,
        featureType = "site"
      )

      exm_sites <- split(
        x = exm_regions$site,
        f = exm_regions$subregion
      )

      exm_cor <- GetMinPairwiseCor(
        rnaEditCluster_mat = exm_data,
        minPairCorr = 0.1,
        probes_ls = exm_sites,
        method = "spearman"
      )

      SitesToRegion(
        sitesSubregion_df = exm_regions,
        keepminPairwiseCor_df = exm_cor$keepminPairwiseCor_df
      )

[Package rnaEditr version 1.2.0 Index]