IRanges-utils: IRanges utility functions

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

IRanges utility functions

Description

Utility functions for creating or modifying IRanges objects.

Usage

## Create an IRanges instance:
successiveIRanges(width, gapwidth=0, from=1)
breakInChunks(totalsize, nchunk, chunksize)

## Turn a logical vector into a set of ranges:
whichAsIRanges(x)

## Coercion:
asNormalIRanges(x, force=TRUE)

Arguments

width	A vector of non-negative integers (with no NAs) specifying the widths of the ranges to create.
gapwidth	A single integer or an integer vector with one less element than the width vector specifying the widths of the gaps separating one range from the next one.
from	A single integer specifying the starting position of the first range.
totalsize	A single non-negative integer. The total size of the object to break.
nchunk	A single positive integer. The number of chunks.
chunksize	A single positive integer. The size of the chunks (last chunk might be smaller).
x	A logical vector for whichAsIRanges. An IRanges object for asNormalIRanges.
force	TRUE or FALSE. Should x be turned into a NormalIRanges object even if isNormal(x) is FALSE?

Details

successiveIRanges returns an IRanges instance containing the ranges that have the widths specified in the width vector and are separated by the gaps specified in gapwidth. The first range starts at position from. When gapwidth=0 and from=1 (the defaults), the returned IRanges can be seen as a partitioning of the 1:sum(width) interval. See ?Partitioning for more details on this.

breakInChunks returns a PartitioningByEnd object describing the "chunks" that result from breaking a vector-like object of length totalsize in the chunks described by nchunk or chunksize.

whichAsIRanges returns an IRanges instance containing all of the ranges where x is TRUE.

If force=TRUE (the default), then asNormalIRanges will turn x into a NormalIRanges instance by reordering and reducing the set of ranges if necessary (i.e. only if isNormal(x) is FALSE, otherwise the set of ranges will be untouched). If force=FALSE, then asNormalIRanges will turn x into a NormalIRanges instance only if isNormal(x) is TRUE, otherwise it will raise an error. Note that when force=FALSE, the returned object is guaranteed to contain exactly the same set of ranges than x. as(x, "NormalIRanges") is equivalent to asNormalIRanges(x, force=TRUE).

Author(s)

Hervé Pagès

See Also

• IRanges objects.

• Partitioning objects.

• equisplit for splitting a list-like object into a specified number of partitions.

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

• setops-methods for performing set operations on IRanges objects.

• solveUserSEW

• successiveViews

Examples

vec <- as.integer(c(19, 5, 0, 8, 5))

successiveIRanges(vec)

breakInChunks(600999, chunksize=50000)  # chunks of size 50000 (last
                                        # chunk is smaller)

whichAsIRanges(vec >= 5)

x <- IRanges(start=c(-2L, 6L, 9L, -4L, 1L, 0L, -6L, 10L),
             width=c( 5L, 0L, 6L,  1L, 4L, 3L,  2L,  3L))
asNormalIRanges(x)  # 3 non-empty ranges ordered from left to right and
                    # separated by gaps of width >= 1.

## More on normality:
example(`IRanges-class`)
isNormal(x16)                        # FALSE
if (interactive())
    x16 <- asNormalIRanges(x16)      # Error!
whichFirstNotNormal(x16)             # 57
isNormal(x16[1:56])                  # TRUE
xx <- asNormalIRanges(x16[1:56])
class(xx)
max(xx)
min(xx)

Bioconductor/IRanges documentation built on Dec. 7, 2024, 1:19 p.m.