Description Usage Arguments Details Value Author(s) See Also Examples

`bpvec`

applies `FUN`

to subsets of `X`

. Any type of
object `X`

is allowed, provided `length`

, and `[`

are
defined on `X`

. `FUN`

is a function such that
`length(FUN(X)) == length(X)`

. The objects returned by `FUN`

are concatenated by `AGGREGATE`

(`c()`

by default). The
return value is `FUN(X)`

.

1 |

`X` |
Any object for which methods |

`FUN` |
A function to be applied to subsets of |

`...` |
Additional arguments for |

`AGGREGATE` |
A function taking any number of arguments |

`BPPARAM` |
An optional |

`BPREDO` |
A |

This method creates a vector of indices for `X`

that divide the
elements as evenly as possible given the number of `bpworkers()`

and `bptasks()`

of `BPPARAM`

. Indices and data are passed to
`bplapply`

for parallel evaluation.

The distinction between `bpvec`

and `bplapply`

is that
`bplapply`

applies `FUN`

to each element of `X`

separately whereas `bpvec`

assumes the function is vectorized,
e.g., `c(FUN(x[1]), FUN(x[2]))`

is equivalent to
`FUN(x[1:2])`

. This approach can be more efficient than
`bplapply`

but requires the assumption that `FUN`

takes a
vector input and creates a vector output of the same length as the
input which does not depend on partitioning of the vector. This
behavior is consistent with `parallel:::pvec`

and the
`?pvec`

man page should be consulted for further details.

The result should be identical to `FUN(X, ...)`

(assuming that
`AGGREGATE`

is set appropriately).

When evaluation of individual elements of `X`

results in an
error, the result is a `list`

with the same geometry (i.e.,
`lengths()`

) as the split applied to `X`

to create chunks
for parallel evaluation; one or more elements of the list contain a
`bperror`

element, indicting that the vectorized calculation
failed for at least one of the index values in that chunk.

An error is also signaled when `FUN(X)`

does not return an
object of the same length as `X`

; this condition is only detected
when the number of elements in `X`

is greater than the number of
workers.

Martin Morgan mailto:mtmorgan@fhcrc.org.

`bplapply`

for parallel lapply.

`BiocParallelParam`

for possible values of `BPPARAM`

.

`pvec`

for background.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
methods("bpvec")
## ten tasks (1:10), called with as many back-end elements are specified
## by BPPARAM. Compare with bplapply
fun <- function(v) {
message("working")
sqrt(v)
}
system.time(result <- bpvec(1:10, fun))
result
## invalid FUN -- length(class(X)) is not equal to length(X)
bptry(bpvec(1:2, class, BPPARAM=SerialParam()))
``` |

BiocParallel documentation built on Nov. 8, 2020, 5:46 p.m.

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