extractListFragments: Extract list fragments from a list-like object

In Bioconductor/IRanges: Foundation of integer range manipulation in Bioconductor

Extract list fragments from a list-like object

Description

Utilities for extracting list fragments from a list-like object.

Usage

extractListFragments(x, aranges, use.mcols=FALSE,
                     msg.if.incompatible=INCOMPATIBLE_ARANGES_MSG)

equisplit(x, nchunk, chunksize, use.mcols=FALSE)

Arguments

x	The list-like object from which to extract the list fragments. Can be any List derivative for extractListFragments. Can also be an ordinary list if extractListFragments is called with use.mcols=TRUE. Can be any List derivative that supports relist() for equisplit.
aranges	An IntegerRanges derivative containing the absolute ranges (i.e. the ranges along unlist(x)) of the list fragments to extract. The ranges in aranges must be compatible with the cumulated length of all the list elements in x, that is, start(aranges) and end(aranges) must be >= 1 and <= sum(elementNROWS(x)), respectively. Also please note that only IntegerRanges objects that are disjoint and sorted are supported at the moment.
use.mcols	Whether to propagate the metadata columns on x (if any) or not. Must be TRUE or FALSE (the default). If set to FALSE, instead of having the metadata columns propagated from x, the object returned by extractListFragments has metadata columns revmap and revmap2, and the object returned by equisplit has metadata column revmap. Note that this is the default.
msg.if.incompatible	The error message to use if aranges is not compatible with the cumulated length of all the list elements in x.
nchunk	The number of chunks. Must be a single positive integer.
chunksize	The size of the chunks (last chunk might be smaller). Must be a single positive integer.

Details

A list fragment of list-like object x is a window in one of its list elements.

extractListFragments is a low-level utility that extracts list fragments from list-like object x according to the absolute ranges in aranges.

equisplit fragments and splits list-like object x into a specified number of partitions with equal (total) width. This is useful for instance to ensure balanced loading of workers in parallel evaluation. For example, if x is a GRanges object, each partition is also a GRanges object and the set of all partitions is returned as a GRangesList object.

Value

An object of the same class as x for extractListFragments.

An object of class relistToClass(x) for equisplit.

Author(s)

Hervé Pagès

See Also

• IRanges and IRangesList objects.

• Partitioning objects.

• IntegerList objects.

• breakInChunks from breaking a vector-like object in chunks.

• GRanges and GRangesList objects defined in the GenomicRanges package.

• List objects defined in the S4Vectors package.

• intra-range-methods and inter-range-methods for intra range and inter range transformations.

Examples

## ---------------------------------------------------------------------
## A. extractListFragments()
## ---------------------------------------------------------------------

x <- IntegerList(a=101:109, b=5:-5)
x

aranges <- IRanges(start=c(2, 4, 8, 17, 17), end=c(3, 6, 14, 16, 19))
aranges
extractListFragments(x, aranges)

x2 <- IRanges(c(1, 101, 1001, 10001), width=c(10, 5, 0, 12),
              names=letters[1:4])
mcols(x2)$label <- LETTERS[1:4]
x2

aranges <- IRanges(start=13, end=20)
extractListFragments(x2, aranges)
extractListFragments(x2, aranges, use.mcols=TRUE)

aranges2 <- PartitioningByWidth(c(3, 9, 13, 0, 2))
extractListFragments(x2, aranges2)
extractListFragments(x2, aranges2, use.mcols=TRUE)

x2b <- as(x2, "IntegerList")
extractListFragments(x2b, aranges2)

x2c <- as.list(x2b)
extractListFragments(x2c, aranges2, use.mcols=TRUE)

## ---------------------------------------------------------------------
## B. equisplit()
## ---------------------------------------------------------------------

## equisplit() first calls breakInChunks() internally to create a
## PartitioningByWidth object that contains the absolute ranges of the
## chunks, then calls extractListFragments() on it 'x' to extract the
## fragments of 'x' that correspond to these absolute ranges. Finally
## the IRanges object returned by extractListFragments() is split into
## an IRangesList object where each list element corresponds to a chunk.
equisplit(x2, nchunk=2)
equisplit(x2, nchunk=2, use.mcols=TRUE)

equisplit(x2, chunksize=5)

library(GenomicRanges)
gr <- GRanges(c("chr1", "chr2"), IRanges(1, c(100, 1e5)))
equisplit(gr, nchunk=2)
equisplit(gr, nchunk=1000)

## ---------------------------------------------------------------------
## C. ADVANCED extractListFragments() EXAMPLES
## ---------------------------------------------------------------------

## === D1. Fragment list-like object into length 1 fragments ===

## First we construct a Partitioning object where all the partitions
## have a width of 1:
x2_cumlen <- nobj(PartitioningByWidth(x2))  # Equivalent to
                                            # length(unlist(x2)) except
                                            # that it doesn't unlist 'x2'
                                            # so is much more efficient.
aranges1 <- PartitioningByEnd(seq_len(x2_cumlen))
aranges1

## Then we use it to fragment 'x2':
extractListFragments(x2, aranges1)
extractListFragments(x2b, aranges1)
extractListFragments(x2c, aranges1, use.mcols=TRUE)

## === D2. Fragment a Partitioning object ===

partitioning2 <- PartitioningByEnd(x2b)  # same as PartitioningByEnd(x2)
extractListFragments(partitioning2, aranges2)

## Note that when the 1st arg is a Partitioning derivative, then
## swapping the 1st and 2nd elements in the call to extractListFragments()
## doesn't change the returned partitioning:
extractListFragments(aranges2, partitioning2)

## ---------------------------------------------------------------------
## D. SANITY CHECKS
## ---------------------------------------------------------------------

## If 'aranges' is 'PartitioningByEnd(x)' or 'PartitioningByWidth(x)'
## and 'x' has no zero-length list elements, then
## 'extractListFragments(x, aranges, use.mcols=TRUE)' is a no-op.
check_no_ops <- function(x) {
  aranges <- PartitioningByEnd(x)
  stopifnot(identical(
    extractListFragments(x, aranges, use.mcols=TRUE), x
  ))
  aranges <- PartitioningByWidth(x)
  stopifnot(identical(
    extractListFragments(x, aranges, use.mcols=TRUE), x
  ))
}

check_no_ops(x2[lengths(x2) != 0])
check_no_ops(x2b[lengths(x2b) != 0])
check_no_ops(x2c[lengths(x2c) != 0])
check_no_ops(gr)

Bioconductor/IRanges documentation built on Feb. 11, 2024, 8:11 p.m.