SingleCoeditedRegion: Extracts contiguous co-edited genomic regions from a single...
In rnaEditr: Statistical analysis of RNA editing sites and hyper-editing regions

Description Usage Arguments Value Examples

Extracts contiguous co-edited genomic regions from an input genomic region.

SingleCoeditedRegion(
  region_df,
  rnaEditMatrix,
  output = c("GRanges", "dataframe"),
  rDropThresh_num = 0.4,
  minPairCorr = 0.1,
  minSites = 3,
  method = c("spearman", "pearson"),
  minEditFreq = 0.05,
  returnAllSites = FALSE,
  verbose = TRUE
)

`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 on 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)`).
`output`	Type of output data, can be "GRanges" or "dataframe". Defaults to "GRanges".
`rDropThresh_num`	Threshold for minimum correlation between RNA editing levels of one site and the mean RNA editing levels of the rest of the sites. Please set a number between 0 and 1. Defaults to 0.4.
`minPairCorr`	Minimum pairwise correlation coefficient of a cluster is used as a filter to select clusters for output. Only clusters with all pairwise correlations between sites more than `minPairCorr` will be selected for output. To use this filter, set this argument to a number between -1 and 1 (defaults to 0.1). To turn it off, please set the argument to -1.
`minSites`	Minimum number of sites to be considered a region. Only regions with more than `minSites` number of sites will be returned.
`method`	Method for computing correlations. Defaults to `"spearman"`.
`minEditFreq`	Threshold for minimum percentage of 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.
`returnAllSites`	When no co-edited region is found in an input genomic region, `returnAllSites = TRUE` indicates outputting all the sites from the input region, while `returnAllSites = FALSE` indicates not returning any site from the input region. Defaults to FALSE.
`verbose`	Should messages and warnings be displayed? Defaults to TRUE, but is set to FALSE when called from within `AllCoeditedRegions()`.

When output is set to "GRanges", a GRanges object with seqnames, ranges and strand of the contiguous co-edited regions will be returned.

When output is set to "dataframe", a data frame with following columns will be returned:

site : site ID.
chr : chromosome.
pos : genomic location.
r_drop : the correlation between RNA editing levels of one site and the mean RNA editing levels of the rest of the sites.
keep : indicator for co-edited sites, The sites with keep = 1 belong to the contiguous and co-edited region.
keep_contiguous : contiguous co-edited region number.
regionMinPairwiseCor : the minimum pairwise correlation of a co-edited region.
keep_regionMinPairwiseCor : equals 1 for contiguous co-edited subregions. The regions with keepminPairwiseCor = 1 are the ones that passed the regionMinPairwiseCor filter and will be returned as a co-edited sub-region.

  data(rnaedit_df)
  
  exm_region <- data.frame(
    seqnames = "chr1",
    start =  28691093,
    end = 28826881, 
    stringsAsFactors = FALSE
  )
  
  SingleCoeditedRegion(
    region_df = exm_region,
    rnaEditMatrix = rnaedit_df,
    minPairCorr = 0.25,
    output = "dataframe",
    method = "spearman"
  )