inst/demo_srcs/IRanges/R/RleViewsList-utils.R

In vjcitn/BiocQE: Bioconductor Quality Enhancement

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### The "viewApply", "viewMins", "viewMaxs", and "viewSums" generics and
### methods.
###

setMethod("viewApply", "RleViewsList",
          function(X, FUN, ..., simplify = TRUE) {
            ans_listData <- lapply(structure(seq_along(X), names=names(X)),
              function(i) {
                ans_elt <- aggregate(
                             subject(X[[i]]),
                             start=structure(start(X[[i]]),
                                             names=names(start(X[[i]]))),
                             end=end(X[[i]]),
                             FUN=FUN,
                             ...,
                             simplify=simplify)
                if (!simplify)
                  ans_elt <- S4Vectors:::new_SimpleList_from_list("SimpleList",
                                                     ans_elt,
                                                     metadata=metadata(X[[i]]),
                                                     mcols=mcols(X[[i]], use.names=FALSE))
                ans_elt
              })
            S4Vectors:::new_SimpleList_from_list("SimpleList", ans_listData,
                                                 metadata=metadata(X),
                                                 mcols=mcols(X, use.names=FALSE))})

.summaryRleViewsList <- function(x, FUN, na.rm = FALSE, outputListType = NULL)
{
    FUN <- match.fun(FUN)
    if (length(x) == 0) {
        outputListType <- "SimpleList"
        listData <- list()
    } else {
        if (is.null(outputListType)) {
            valuesClass <- class(runValue(subject(x[[1L]])))
            if (valuesClass == "integer" || valuesClass == "logical")
                outputListType <- "SimpleIntegerList"
            else if (valuesClass == "numeric")
                outputListType <- "SimpleNumericList"
            else
                stop("cannot compute numeric summary over a non-numeric Rle")
        }
        listData <-
          lapply(structure(seq_len(length(x)), names = names(x)),
                 function(i) FUN(x[[i]], na.rm = na.rm))
    }
    S4Vectors:::new_SimpleList_from_list(outputListType, listData,
                                         metadata = metadata(x),
                                         mcols = mcols(x, use.names=FALSE))
}
setMethod("viewMins", "RleViewsList",
          function(x, na.rm = FALSE)
          .summaryRleViewsList(x, FUN = viewMins, na.rm = na.rm))

setMethod("viewMaxs", "RleViewsList",
          function(x, na.rm = FALSE)
          .summaryRleViewsList(x, FUN = viewMaxs, na.rm = na.rm))

setMethod("viewSums", "RleViewsList",
          function(x, na.rm = FALSE)
          .summaryRleViewsList(x, FUN = viewSums, na.rm = na.rm))

setMethod("viewMeans", "RleViewsList",
          function(x, na.rm = FALSE)
          .summaryRleViewsList(x, FUN = viewMeans, na.rm = na.rm,
                               outputListType = "SimpleNumericList"))

setMethod("viewWhichMins", "RleViewsList",
          function(x, na.rm = FALSE)
          .summaryRleViewsList(x, FUN = viewWhichMins, na.rm = na.rm,
                               outputListType = "SimpleIntegerList"))

setMethod("viewWhichMaxs", "RleViewsList",
          function(x, na.rm = FALSE)
          .summaryRleViewsList(x, FUN = viewWhichMaxs, na.rm = na.rm,
                               outputListType = "SimpleIntegerList"))

setMethod("viewRangeMaxs", "RleViewsList",
          function(x, na.rm = FALSE)
          .summaryRleViewsList(x, FUN = viewRangeMaxs, na.rm = na.rm,
                               outputListType = "SimpleIRangesList"))

setMethod("viewRangeMins", "RleViewsList",
          function(x, na.rm = FALSE)
          .summaryRleViewsList(x, FUN = viewRangeMins, na.rm = na.rm,
                               outputListType = "SimpleIRangesList"))