SummarizeSingleRegion: Summarizes RNA editing levels from multiple sites in a single...

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

Summarizes RNA editing levels from multiple sites in a single region.

Description

Summarizes RNA editing levels from multiple sites in an input region.

Usage

SummarizeSingleRegion(
  region_df,
  rnaEditMatrix,
  selectMethod = MedianSites,
  ...
)

Arguments

region_df	A data frame with the input genomic region. Please make sure columns seqnames, start, and end are included in the data frame.
rnaEditMatrix	A matrix (or data frame) of RNA editing level values for individual sites, with row names as site IDs in the form of "chrAA:XXXXXXXX", and column names as sample IDs. Please make sure to follow the format of example dataset (data(rnaedit_df)).
selectMethod	Method for summarizing regions. Available options are "MaxSites", "MeanSites", "MedianSites", "PC1Sites". Please see RegionSummaryMethod for more details.
...	Dots for additional internal arguments (currently unused).

Value

A named numeric vector of summarized RNA editing levels with sample IDs as column names.

Examples

  data(rnaedit_df)
  
  exm_region <- data.frame(
    seqnames = "chr1",
    start =  28691093,
    end = 28826881, 
    stringsAsFactors = FALSE
  )
   
  SummarizeSingleRegion(
    region_df = exm_region,
    rnaEditMatrix = rnaedit_df
  )[1:3]

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