AnnotateResults: Add Annotations to site-specific or region-based analysis...

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

Add Annotations to site-specific or region-based analysis results.

Description

Add annotations to site-specific or region-based analysis results from function TestAssociations.

Usage

AnnotateResults(
  results_df,
  closeByRegions_gr = NULL,
  inputRegions_gr = NULL,
  genome = c("hg38", "hg19"),
  analysis = c("region-based", "site-specific")
)

Arguments

results_df	An output data frame from function TestAssociations, which includes variables for locations and result of statistical tests for the genomic sites or regions.
closeByRegions_gr	An output GRanges object from function AllCloseByRegions, defaults to NULL.
inputRegions_gr	A GRanges object for input genomic regions, defaults to NULL.
genome	Use "hg19" or "hg38" gene reference. Defaults to "hg38".
analysis	Results type. Defaults to "region-based". When it's set to "site-specific", arguments closeByRegions_gr and inputRegions_gr will not be used and set to NULL automatically.

Value

A data frame with locations of the genomic sites or regions (seqnames, start, end, width), annotations for locations (inputRegion, closeByRegion, symbol), test statistics (estimate, stdErr or coef, exp_coef, se_coef), pValue and false discovery rate (fdr).

See Also

TransformToGR, AllCloseByRegions, AllCoeditedRegions, CreateEditingTable, SummarizeAllRegions, TestAssociations

Examples

  data(rnaedit_df)
  
  # get GRanges for genes
  genes_gr <- TransformToGR(
    genes_char = c("PHACTR4", "CCR5", "METTL7A"),
    type = "symbol",
    genome = "hg19"
  )
  
  # find close-by regions within the genes
  closebyRegions_gr <- AllCloseByRegions(
    regions_gr = genes_gr,
    rnaEditMatrix = rnaedit_df
  )
  
  # identify co-edited regions within the genes 
  coedited_gr <- AllCoeditedRegions(
    regions_gr = closebyRegions_gr,
    rnaEditMatrix = rnaedit_df,
    output = "GRanges",
    method = "spearman"
  )
  
  # summarize editing levels within each gene by maximum
  summarizedRegions_df <- SummarizeAllRegions(
    regions_gr = coedited_gr,
    rnaEditMatrix = rnaedit_df,
    selectMethod = MaxSites
  )
  
  exm_pheno <- readRDS(
    system.file(
    "extdata",
    "pheno_df.RDS",
    package = 'rnaEditr',
    mustWork = TRUE
    )
  )
  
  # test summarized editing levels against survival outcome
  results_df <- TestAssociations(
    rnaEdit_df = summarizedRegions_df,
    pheno_df = exm_pheno,
    responses_char = "sample_type",
    covariates_char = NULL,
    respType = "binary"
  )
  
  AnnotateResults(
    results_df = results_df,
    closeByRegions_gr = closebyRegions_gr,
    inputRegions_gr = genes_gr,
    genome = "hg19"
  )
  

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