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

Description Usage Arguments Value See Also Examples

View source: R/SummarizeAllRegions.R

Description

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

Usage

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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

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  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]

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