bpaggregate: Apply a function on subsets of data frames
In Bioconductor/BiocParallel: Bioconductor facilities for parallel evaluation

bpaggregate

R Documentation

Apply a function on subsets of data frames

Description

This is a parallel version of aggregate.

Usage


## S4 method for signature 'formula,BiocParallelParam'
bpaggregate(x, data, FUN, ...,
    BPREDO=list(), BPPARAM=bpparam(), BPOPTIONS = bpoptions())

## S4 method for signature 'data.frame,BiocParallelParam'
bpaggregate(x, by, FUN, ...,
    simplify=TRUE, BPREDO=list(), BPPARAM=bpparam(), BPOPTIONS = bpoptions())

## S4 method for signature 'matrix,BiocParallelParam'
bpaggregate(x, by, FUN, ...,
    simplify=TRUE, BPREDO=list(),
    BPPARAM=bpparam(), BPOPTIONS = bpoptions()
)

## S4 method for signature 'ANY,missing'
bpaggregate(x, ..., BPREDO=list(),
    BPPARAM=bpparam(), BPOPTIONS = bpoptions()
)

Arguments

`x`	A `data.frame`, `matrix` or a formula.
`by`	A list of factors by which `x` is split; applicable when `x` is `data.frame` or `matrix`.
`data`	A `data.frame`; applicable when `x` is a `formula`.
`FUN`	Function to apply.
`...`	Additional arguments for `FUN`.
`simplify`	If set to `TRUE`, the return values of `FUN` will be simplified using `simplify2array`.
`BPPARAM`	An optional `BiocParallelParam` instance determining the parallel back-end to be used during evaluation.
`BPREDO`	A `list` of output from `bpaggregate` with one or more failed elements. When a list is given in `BPREDO`, `bpok` is used to identify errors, tasks are rerun and inserted into the original results.
`BPOPTIONS`	Additional options to control the behavior of the parallel evaluation, see `bpoptions`.

Details

bpaggregate is a generic with methods for data.frame matrix and formula objects. x is divided into subsets according to factors in by. Data chunks are sent to the workers, FUN is applied and results are returned as a data.frame.

The function is similar in spirit to aggregate from the stats package but aggregate is not explicitly called. The bpaggregate formula method reformulates the call and dispatches to the data.frame method which in turn distributes data chunks to workers with bplapply.

Value

See aggregate.

Author(s)

Martin Morgan mailto:mtmorgan@fhcrc.org.

Examples


if (interactive() && require(Rsamtools) && require(GenomicAlignments)) {

  fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
  param <- ScanBamParam(what = c("flag", "mapq"))
  gal <- readGAlignments(fl, param=param)

  ## Report the mean map quality by range cutoff:
  cutoff <- rep(0, length(gal))
  cutoff[start(gal) > 1000 & start(gal) < 1500] <- 1
  cutoff[start(gal) > 1500] <- 2
  bpaggregate(as.data.frame(mcols(gal)$mapq), list(cutoff = cutoff), mean)

}

Bioconductor/BiocParallel documentation built on Oct. 31, 2024, 6:58 a.m.