rdapply: Applying over spaces

Description

WARNING: RDApplyParams objects and the rdapply() function are deprecated!

The rdapply function applies a user function over the spaces of a RangedData. The parameters to rdapply are collected into an instance of RDApplyParams, which is passed as the sole parameter to rdapply.

Usage

rdapply(x, ...)

Arguments

The RDApplyParams instance, see below for how to make one.

...

Additional arguments for methods

Value

By default a list holding the result of each invocation of the user function, but see details.

Details

The rdapply function is an attempt to facilitate the common operation of performing the same operation over each space (e.g. chromosome) in a RangedData. To facilitate a wide array of such tasks, the function takes a large number of options. The RDApplyParams class is meant to help manage this complexity. In particular, it facilitates experimentation through its support for incremental changes to parameter settings. There are two RangedData settings that are required: the user function object and the RangedData over which it is applied. The rest of the settings determine what is actually passed to the user function and how the return value is processed before relaying it to the user. The following is the description and rationale for each setting.

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Examples

Run this code

## WARNING: RDApplyParams objects and the rdapply() function are
## deprecated!

ranges <- IRanges(c(1,2,3),c(4,5,6))
  score <- c(2L, 0L, 1L)
  rd <- RangedData(ranges, score, space = c("chr1","chr2","chr1"))
  
  ## a single function
  countrows <- function(rd) nrow(rd)
  params <- RDApplyParams(rd, countrows)
  rdapply(params) # list(chr1 = 2L, chr2 = 1L)

  ## with a parameter
  params <- RDApplyParams(rd, function(rd, x) nrow(rd)*x, list(x = 2))
  rdapply(params) # list(chr1 = 4L, chr2 = 2L)

  ## add a filter
  cutoff <- 0
  rules <- FilterRules(filter = score > cutoff)
  params <- RDApplyParams(rd, countrows, filterRules = rules)
  rdapply(params) # list(chr1 = 2L, chr2 = 0L)
  rules <- FilterRules(list(fun = function(rd) rd[["score"]] < 2),
                       filter = score > cutoff)
  params <- RDApplyParams(rd, countrows, filterRules = rules)
  rdapply(params) # list(chr1 = 1L, chr2 = 0L)
  active(filterRules(params))["filter"] <- FALSE
  rdapply(params) # list(chr1 = 1L, chr2 = 1L)

  ## simplify
  params <- RDApplyParams(rd, countrows, simplify = TRUE)
  rdapply(params) # c(chr1 = 2L, chr2 = 1L)

  ## reducing
  params <- RDApplyParams(rd, countrows, reducerFun = unlist,
                          reducerParams = list(use.names = FALSE))
  rdapply(params) ## c(2L, 1L)