SummarizeAllRegions: Summarize RNA editing levels from multiple sites in regions.

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

Summarize RNA editing levels from multiple sites in regions.

Description

A wrapper function to summarize RNA editing levels from multiple sites in regions.

Usage

SummarizeAllRegions(
  regions_gr,
  rnaEditMatrix,
  selectMethod = MedianSites,
  progressBar = "time",
  ...
)

Arguments

regions_gr	A GRanges object of input genomic regions.
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.
progressBar	Name of the progress bar to use. There are currently five types of progress bars: "time", "none", "text", "tk", and "win". Defaults to "time". See create_progress_bar for more details.
...	Dots for additional internal arguments (currently unused).

Value

A data frame of the class rnaEdit_df, includes variables seqnames, start, end, width and summarized RNA editing levels in each sample.

See Also

TransformToGR, AllCloseByRegions, AllCoeditedRegions, CreateEditingTable, TestAssociations, AnnotateResults

Examples

  data(rnaedit_df)
  
  genes_gr <- TransformToGR(
    genes_char = c("PHACTR4", "CCR5", "METTL7A"),
    type = "symbol",
    genome = "hg19"
  )
  
  exm_regions <- AllCoeditedRegions(
    regions_gr = genes_gr,
    rnaEditMatrix = rnaedit_df,
    output = "GRanges",
    method = "spearman"
  )
  
  SummarizeAllRegions(
    regions_gr = exm_regions,
    rnaEditMatrix = rnaedit_df
  )[1:3, 1:6]

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