CreateRdrop: Calculates R-drop values for RNA editing sites.

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

Calculates R-drop values for RNA editing sites.

Description

Calculates the correlation coefficient between RNA editing levels of one site and the mean RNA editing levels of the rest of the sites in a region.

Usage

CreateRdrop(
  data,
  method = c("spearman", "pearson"),
  minEditFreq = 0.05,
  verbose = TRUE
)

Arguments

data	A data frame 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".
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.

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.

Examples

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

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