AllCoeditedRegions {rnaEditr} | R Documentation

## Extracts contiguous co-edited genomic regions from input genomic regions .

### Description

A wrapper function to extract contiguous co-edited genomic regions from input genomic regions.

### Usage

    AllCoeditedRegions(
      regions_gr,
      rnaEditMatrix,
      output = c("GRanges", "dataframe"),
      rDropThresh_num = 0.4,
      minPairCorr = 0.1,
      minSites = 3,
      method = c("spearman", "pearson"),
      returnAllSites = FALSE,
      progressBar = "time",
      verbose = TRUE
    )

### 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)`).
`output` | Type of output data. Defaults to `"GRanges"`.
`rDropThresh_num` | Threshold for minimum correlation between RNA editing levels of one site and the mean RNA editing levels of the rest of the sites. Please set a number between 0 and 1. Defaults to 0.4.
`minPairCorr` | Threshold for minimum pairwise correlation of sites within a selected cluster. To use this filter, set a number between -1 and 1 (defaults to 0.1). To select all clusters (i.e. no filter), please set this argument to -1.
`minSites` | Minimum number of sites to be considered as a region. Only regions with more than `minSites` number of sites will be returned.
`method` | Method for computing correlation. Defaults to `"spearman"`.
`returnAllSites` | When no contiguous co-edited regions are found in an input genomic region, `returnAllSites = TRUE` indicates returning all the sites in the input region, while `returnAllSites = FALSE` indicates not returning any site from input region. Defaults to FALSE.
`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.
`verbose` | Should messages and warnings be displayed? Defaults to FALSE, but is set to TRUE when called from within `SingleCoeditedRegion()`.

### Value

When `output` is set as `"GRanges"`, a GRanges object with `seqnames`, `ranges` and `strand` of the contiguous co-edited regions will be returned. When `output` is set as `"dataframe"`, a data frame with following columns will be returned:

- `site` : site ID.

- `chr` : chromosome number.

- `pos` : genomic position number.

- `r_drop` : the correlation between RNA editing levels of one site and the mean RNA editing levels of the rest of the sites.

- `keep` : indicator for co-edited sites, the sites with `keep = 1` belong to the contiguous and co-edited region.

- `keep_contiguous` : contiguous co-edited region number.

- `regionMinPairwiseCor` : the pairwise correlation of a subregion.

- `keep_regionMinPairwiseCor` : indicator for contiguous co-edited subregions, the regions with `keepminPairwiseCor = 1` passed the minimum correlation and will be returned as a contiguous co-edited subregion.

### See Also

`TransformToGR`, `AllCloseByRegions`, `CreateEditingTable`, `SummarizeAllRegions`, `TestAssociations`, `AnnotateResults`

### Examples

      data(rnaedit_df)

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

      AllCoeditedRegions(
        regions_gr = genes_gr,
        rnaEditMatrix = rnaedit_df,
        output = "GRanges",
        method = "spearman"
      )

[Package rnaEditr version 1.4.0 Index]