SingleCoeditedRegion {rnaEditr} | R Documentation

## Extracts contiguous co-edited genomic regions from a single genomic region.

### Description

Extracts contiguous co-edited genomic regions from an input genomic region.

### Usage

    SingleCoeditedRegion(
      region_df,
      rnaEditMatrix,
      output = c("GRanges", "dataframe"),
      rDropThresh_num = 0.4,
      minPairCorr = 0.1,
      minSites = 3,
      method = c("spearman", "pearson"),
      minEditFreq = 0.05,
      returnAllSites = FALSE,
      verbose = TRUE
    )

### 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 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, can be "GRanges" or "dataframe". 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` | Minimum pairwise correlation coefficient of a cluster is used as a filter to select clusters for output. Only clusters with all pairwise correlations between sites more than `minPairCorr` will be selected for output. To use this filter, set this argument to a number between -1 and 1 (defaults to 0.1). To turn it off, please set the argument to -1.
`minSites` | Minimum number of sites to be considered a region. Only regions with more than `minSites` number of sites will be returned.
`method` | Method for computing correlations. Defaults to `"spearman"`.
`minEditFreq` | Threshold for minimum percentage of samples for a given site. The `r_drop` value of the sites with frequency lower than `minEditFreq` will be set as NA. Please set a number between 0 and 1. Defaults to 0.05.
`returnAllSites` | When no co-edited region is found in an input genomic region, `returnAllSites = TRUE` indicates outputting all the sites from the input region, while `returnAllSites = FALSE` indicates not returning any site from the input region. Defaults to FALSE.
`verbose` | Should messages and warnings be displayed? Defaults to TRUE, but is set to FALSE when called from within `AllCoeditedRegions()`.

### Value

When `output` is set to `"GRanges"`, a GRanges object with `seqnames`, `ranges` and `strand` of the contiguous co-edited regions will be returned.

When `output` is set to `"dataframe"`, a data frame with following columns will be returned:

- `site` : site ID.

- `chr` : chromosome.

- `pos` : genomic location.

- `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 minimum pairwise correlation of a co-edited region.

- `keep_regionMinPairwiseCor` : equals 1 for contiguous co-edited subregions. The regions with `keepminPairwiseCor = 1` are the ones that passed the `regionMinPairwiseCor` filter and will be returned as a co-edited sub-region.

### Examples

      data(rnaedit_df)

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

      SingleCoeditedRegion(
        region_df = exm_region,
        rnaEditMatrix = rnaedit_df,
        minPairCorr = 0.25,
        output = "dataframe",
        method = "spearman"
      )

[Package rnaEditr version 1.4.0 Index]