MarkCoeditedSites: Mark RNA editing sites in contiguous and co-edited region.

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

Mark RNA editing sites in contiguous and co-edited region.

Description

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.

Usage

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

Arguments

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.

Details

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.

Value

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.

See Also

CreateRdrop

Examples

  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"
  )
   

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