SummarizeAllRegions {rnaEditr} | R Documentation

## Summarize RNA editing levels from multiple sites in regions.

### Description

A wrapper function to summarize RNA editing levels from multiple sites in regions.

### Usage

    SummarizeAllRegions(
      regions_gr,
      rnaEditMatrix,
      selectMethod = MedianSites,
      progressBar = "time",
      ...
    )

### Arguments

`regions_gr` | A GRanges object of input genomic regions.
`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)`).
`selectMethod` | Method for summarizing regions. Available options are `"MaxSites", "MeanSites", "MedianSites", "PC1Sites"`. Please see `RegionSummaryMethod` for more details.
`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.
`...` | Dots for additional internal arguments (currently unused).

### Value

A data frame of the class `rnaEdit_df`, includes variables `seqnames, start, end, width` and summarized RNA editing levels in each sample.

### See Also

`TransformToGR`, `AllCloseByRegions`, `AllCoeditedRegions`, `CreateEditingTable`, `TestAssociations`, `AnnotateResults`

### Examples

      data(rnaedit_df)

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

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

      SummarizeAllRegions(
        regions_gr = exm_regions,
        rnaEditMatrix = rnaedit_df
      )[1:3, 1:6]

[Package rnaEditr version 1.2.0 Index]