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

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

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"
  )
   

rnaEditr documentation built on Nov. 8, 2020, 8:26 p.m.