MarkCoeditedSites: Mark RNA editing sites in contiguous and co-edited region.
In rnaEditr: Statistical analysis of RNA editing sites and hyper-editing regions

Description Usage Arguments Details Value See Also Examples

Mark RNA editing sites in contiguous and co-edited region by selecting sites for which r_drop values calculated from inner function CreateRdrop is greater than rDropThresh_num.

MarkCoeditedSites(
  rnaEditCluster_mat,
  rDropThresh_num = 0.4,
  method = c("spearman", "pearson"),
  minEditFreq = 0.05,
  verbose = TRUE
)

`rnaEditCluster_mat`	A matrix of RNA editing level values on individual sites, with row names as sample IDs and column names as site IDs in the form of "chrAA:XXXXXXXX".
`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.
`method`	Method for computing correlation. Defaults to `"spearman"`.
`minEditFreq`	Threshold for minimum percentage of edited 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.
`verbose`	Should messages and warnings be displayed? Defaults to TRUE.

r_drop statistic is used to identify co-edited sites. An outlier site (keep = 0) in a genomic region typically has low correlation with the rest of the sites in a genomic region. The sites with r_drop value greater than rDropThresh_num are marked to have keep = 1. Please see CreateRdrop for more details.

A data frame with the following columns:

site : site ID.
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

site : site ID.
keep : indicator for co-edited sites, The sites with keep = 1 belong to the contiguous and co-edited region.
ind : index for the sites.
r_drop : the correlation between RNA editing levels of one site and the mean RNA editing levels of the rest of the sites.

CreateRdrop

  data(t_rnaedit_df)
   
  ordered_cols <- OrderSitesByLocation(
    sites_char = colnames(t_rnaedit_df),
    output = "vector"
  )
  exm_data <- t_rnaedit_df[, ordered_cols]
  
  MarkCoeditedSites(
    rnaEditCluster_mat = exm_data,
    method = "spearman"
  )