SimpleList-class {IRanges}R Documentation

Simple and Compressed List Classes

Description

The (non-virtual) SimpleList and (virtual) CompressedList classes extend the Sequence virtual class.

Details

The SimpleList and CompressedList classes provide an implementation that subclasses can easily extend. The underlying storage in a SimpleList subclass is a list object. The underlying storage in a CompressedList object is a virtually partitioned vector-like object. For more information on the available methods, see the Sequence man page.

Constructor

The SimpleList class constructor is used to create SimpleList objects:

SimpleList(...): takes possibly named objects as elements for the new SimpleList object.

Coercion

In the following code snippets, x is a SimpleList or CompressedList object.

as.list(x): Copies the elements of x into a new R list object.
unlist(x, recursive = TRUE, use.names = TRUE): Concatenates the elements of x into a single elementType(x) object.

Subsetting

In the following code snippets, x is a SimpleList or CompressedList object.

x[i]: In addition to normal usage, the i parameter can be a RangesList, logical RleList, LogicalList, or IntegerList object to perform subsetting within the list elements rather than across them.
x[i] <- value: In addition to normal usage, the i parameter can be a RangesList, logical RleList, LogicalList, or IntegerList object to perform subsetting within the list elements rather than across them.
seqselect(x, start=NULL, end=NULL, width=NULL): In addition to normal usage, the start parameter can be a RangesList, logical RleList, LogicalList, or IntegerList object to perform sequence extraction within the list elements rather than across them.
seqselect(x, start=NULL, end=NULL, width=NULL) <- value: In addition to normal usage, the start parameter can be a RangesList, logical RleList, LogicalList, or IntegerList object to perform sequence replacement within the list elements rather than across them.

Looping

In the following code snippets, x is a SimpleList or CompressedList object.

aggregate(x, by, FUN, start = NULL, end = NULL, width = NULL, frequency = NULL, delta = NULL, ..., simplify = TRUE)): In addition to normal usage, the by parameter can be a RangesList to aggregate within the list elements rather than across them. When by is a RangesList, the output is either a SimpleAtomicList object, if possible, or a SimpleList object, if not.

Author(s)

P. Aboyoun

See Also

Sequence, AtomicList and RangesList for example implementations

Examples

SimpleList(a = letters, ranges = IRanges(1:10, 1:10))

[Package IRanges version 1.6.16 Index]