R/methods-Bin.R

In VEuPathDB/veupathUtils: General Helper Functions for VEuPathDB Projects

#' Find values that fall within a Bin
#' 
#' Given a numeric vector and a Bin, returns a logical vector indicating if 
#' the value in the input vector falls within the bin.
#' @param values numeric vector
#' @param bin A Bin object
#' @return logical vector
#' @export
setGeneric("whichValuesInBin", 
  function(values, bin) standardGeneric("whichValuesInBin"),
  signature = "bin"
)

#' @export
setMethod("whichValuesInBin", signature("Bin"), function(values, bin) {

  inBin <- (values >= bin@binStart) * (values < bin@binEnd)
  return (as.logical(inBin))

})


#' Find values in a vector that fall within any bins in a BinList
#' 
#' Given a vector of values and a BinList, return a logical vector that 
#' indicates if a value was found in any Bin within the BinList
#' 
#' @param values numeric vector
#' @param binList A BinList object
#' @return logical vector
#' @export 
setGeneric("whichValuesInBinList", 
  function(values, binList) standardGeneric("whichValuesInBinList"),
  signature = "binList"
)

#' @export
setMethod("whichValuesInBinList", signature("BinList"), function(values, binList) {

  inBin <- Reduce(`+`, lapply(binList, whichValuesInBin, values = values))
  return (as.logical(inBin))

})


#' Convert a Bin with character start and end values to numeric
#' 
#' Given a Bin object with binStart and binEnd of class character,
#' convert both to numeric and return the Bin.
#' 
#' @param x Bin
#' @return Bin
#' @export 
setMethod("as.numeric", signature("Bin"), function(x) {
  binNumeric <- Bin(
    binStart = as.numeric(x@binStart),
    binEnd = as.numeric(x@binEnd),
    binLabel = x@binLabel,
    value = x@value
  )
  return(binNumeric)
})


#' Convert bins in a BinList with character start and end values to numeric
#' 
#' Given a BinList object containing Bins that may have a character binStart or binEnd,
#' convert all binStarts and binEnds to numeric and return the BinList.
#' 
#' @param x BinList
#' @return BinList
#' @export 
setMethod("as.numeric", signature("BinList"), function(x) {
  binListNumeric <-  BinList(lapply(x, as.numeric))
  return(binListNumeric)
})