CreateOutputDF {rnaEditr} | R Documentation

## Create output data in the format of data frame.

### Description

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

### Usage

    CreateOutputDF(
      keepSites_df,
      keepContiguousSites_df,
      keepminPairwiseCor_df,
      returnAllSites = FALSE,
      verbose = TRUE
    )

### Arguments

`keepSites_df` | An output data frame from function `MarkCoeditedSites`, with variables `site, keep, ind, r_drop`. Please see `MarkCoeditedSites` for details.
`keepContiguousSites_df` | An output data frame from function `FindCorrelatedRegions` with variables `site, subregion`. Please see `FindCorrelatedRegions` for details.
`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 data frame with following columns:

- `site` : site ID.

- `chr` : chromosome number.

- `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 between sites within a sub-region.

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

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

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

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

      CreateOutputDF(
        keepSites_df = exm_sites,
        keepContiguousSites_df = exm_regions,
        keepminPairwiseCor_df = exm_cor$keepminPairwiseCor_df
      )

[Package rnaEditr version 1.4.0 Index]