R: Applies a function to each file in the file set

dsApply.GenericDataFileSet {R.filesets}

R Documentation

Applies a function to each file in the file set

Description

Applies a function to each file in the file set.

WARNING: dsApply(ds, FUN, ...) will soon be deprecated. Instead, use future_lapply(ds, FUN, ...).

Usage

## S3 method for class 'GenericDataFileSet'
dsApply(ds, IDXS=NULL, DROP=is.null(IDXS), AS=as.list, FUN, ..., args=list(), skip=FALSE,
  verbose=FALSE, .parallel=c("none", "future", "BatchJobs", "BiocParallel::BatchJobs"),
  .control=list(dW = 1))

Arguments

`ds, ds1, ds2`	`GenericDataFileSet`:s.
`IDXS`	A (named) `list`, where each element contains a `vector` data set indices, or an `integer` `vector` of individual elements. If `NULL`, then ... with names as of the data set.
`DROP`	If `FALSE`, the first argument passed to `FUN` is always a `list` of files. If `TRUE`, an single-index element is passed to `FUN` as a file instead of as a `list` containing a single file.
`AS`	(optional) A `function` coercing the first set/group object passed.
`FUN`	A `function`.
`...`	Arguments passed to `FUN`.
`args`	(optional) A `list` of additional arguments passed to `FUN`.
`skip`	If `TRUE`, already processed files are skipped.
`verbose`	See `Verbose`.
`.parallel`	A `character` string specifying what mechanism to use for performing parallel processing, if at all.
`.control`	(internal) A named `list` structure controlling the processing.

Value

Returns a named list where the names are those of argument IDXS.

Author(s)

Henrik Bengtsson

Examples

## Not run: 
 isPackageInstalled <- R.utils::isPackageInstalled

# - - - - - - - - - - - - - - - - - - - - - - - -
# Setting up a file set
# - - - - - - - - - - - - - - - - - - - - - - - -
path <- system.file(package="R.filesets")
ds <- GenericDataFileSet$byPath(path)


# - - - - - - - - - - - - - - - - - - - - - - - -
# Get the size of each file
# - - - - - - - - - - - - - - - - - - - - - - - -
# Alt 1.
res1 <- lapply(ds, FUN=getFileSize)
print(res1)

# Alt 2. (according to current settings; see package startup message)
res2 <- dsApply(ds, FUN=getFileSize)
print(res2)
stopifnot(identical(res2, res1))

# Alt 3. (via an internal loop)
res2 <- dsApply(ds, FUN=getFileSize, .parallel="none")
print(res2)
stopifnot(identical(res2, res1))

# Alt 4. (via BiocParallel + BatchJobs)
if (isPackageInstalled("BiocParallel") && isPackageInstalled("BatchJobs")) {
  res3 <- dsApply(ds, FUN=getFileSize, .parallel="BiocParallel::BatchJobs")
  print(res3)
  stopifnot(identical(res3, res1))
}


## End(Not run)

[Package R.filesets version 2.11.0 Index]