FindCorrelatedRegions: Find contiguous co-edited subregions.

In TransBioInfoLab/rnaEditr: Statistical analysis of RNA editing sites and hyper-editing regions

Find contiguous co-edited subregions.

Description

Find contiguous co-edited subregions based on the output file from function MarkCoeditedSites.

Usage

FindCorrelatedRegions(
  sites_df,
  featureType = c("site", "cpg"),
  minSites_int = 3
)

Arguments

sites_df	An output data frame from function MarkCoeditedSites, with variables site, keep, ind, r_drop. Please see MarkCoeditedSites for details.
featureType	Feature type, Defaults to "site".
minSites_int	An integer indicates the minimum number of sites to be considered a contiguous co-edited region.

Value

A data frame with the following columns:

• site : site ID.

• subregion : index for each output contiguous co-edited 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"
  )
  
  FindCorrelatedRegions(
    sites_df = exm_sites,
    featureType = "site"
  )
   

TransBioInfoLab/rnaEditr documentation built on Nov. 29, 2022, 3:31 p.m.