List-class: List objects
In S4Vectors: Foundation of vector-like and list-like containers in Bioconductor

Description Construction Accessors Coercion Subsetting Author(s) See Also Examples

List objects are Vector objects with a "[[", elementType and elementNROWS method. The List class serves a similar role as list in base R.

It adds one slot, the elementType slot, to the two slots shared by all Vector objects.

The elementType slot is the preferred location for List subclasses to store the type of data represented in the sequence. It is designed to take a character of length 1 representing the class of the sequence elements. While the List class performs no validity checking based on elementType, if a subclass expects elements to be of a given type, that subclass is expected to perform the necessary validity checking. For example, the subclass IntegerList (defined in the IRanges package) has elementType = "integer" and its validity method checks if this condition is TRUE.

To be functional, a class that inherits from List must define at least a "[[" method (in addition to the minimum set of Vector methods).

List objects are typically constructed using one of the 3 following methods:

Use of a constructor function. Many constructor functions are provided for List objects e.g. List, IntegerList, RleList, IntegerRangesList, GRangesList, etc... Which one to use depends on the particular type of List object to construct. The name of a constructor function is always the name of a valid class. If it's the name of a concrete class (e.g. the GRangesList constructor defined in the GenomicRanges package), then the constructor function returns an instance of that class. If it's the name of a virtual class (e.g. the List constructor defined in this package, or the IntegerList or RleList or IntegerRangesList constructors defined in the IRanges package), then the returned object belongs to a concrete subclass of that virtual class. Which subclass exactly depends on each constructor function (see man page of a particular constructor function for the details).
Coercion to List or to a List subclass. Many coercion methods are provided to turn any object into a List object. One general and convenient way to convert any vector-like object into a List is to call as(x, "List"). This will typically yield an object from a subclass of CompressedList.
Use of extractList. This function, defined in the IRanges package, extracts user-specified groups of elements from a vector-like object and returns them in a List (or sometimes list) object.

In the following code snippets, x is a List object.

: length(x): Get the number of list elements in x.
: names(x), names(x) <- value: Get or set the names of the elements in the List.
: mcols(x, use.names=FALSE), mcols(x) <- value: Get or set the metadata columns. See Vector man page for more information.
: elementType(x): Get the scalar string naming the class from which all elements must derive.
: elementNROWS(x): Get the length (or nb of row for a matrix-like object) of each of the elements. Equivalent to sapply(x, NROW).
: isEmpty(x): Returns a logical indicating either if the sequence has no elements or if all its elements are empty.

To List.

as(x, "List"): Converts a vector-like object into a List, usually a CompressedList derivative. One notable exception is when x is an ordinary list, in which case as(x, "List") returns a SimpleList derivative.

To explicitly request a SimpleList derivative, call as(x, "SimpleList").

See ?CompressedList (you might need to load the IRanges package first) and ?SimpleList for more information about the CompressedList and SimpleList representations.

From List. In the code snippets below, x is a List object.

as.list(x, ...), as(from, "list"): Turns x into an ordinary list.

unlist(x, recursive=TRUE, use.names=TRUE): Concatenates the elements of x into a single vector-like object (of class elementType(x)).

as.data.frame(x, row.names=NULL, optional=FALSE , value.name="value", use.outer.mcols=FALSE, group_name.as.factor=FALSE, ...): Coerces a List to a data.frame. The result has the same length as unlisted x with two additional columns, group and group_name. group is an integer that indicates which list element the record came from. group_name holds the list name associated with each record; value is character by default and factor when group_name.as.factor is TRUE.

When use.outer.mcols is TRUE the metadata columns on the outer list elements of x are replicated out and included in the data.frame. List objects that unlist to a single vector (column) are given the column name 'value' by default. A custom name can be provided in value.name.

Splitting values in the resulting data.frame by the original groups in x should be done using the group column as the f argument to splitAsList. To relist data, use x as the skeleton argument to relist.

In the code snippets below, x is a List object.

: x[i]: Return a new List object made of the list elements selected by subscript i. Subscript i can be of any type supported by subsetting of a Vector object (see Vector man page for the details), plus the following types: IntegerList, LogicalList, CharacterList, integer-RleList, logical-RleList, character-RleList, and IntegerRangesList. Those additional types perform subsetting within the list elements rather than across them.
: x[i] <- value: Replacement version of x[i].
: x[[i]]: Return the selected list element i, where i is an numeric or character vector of length 1.
: x[[i]] <- value: Replacement version of x[[i]].
: x$name, x$name <- value: Similar to x[[name]] and x[[name]] <- value, but name is taken literally as an element name.

P. Aboyoun and H. Pagès

splitAsList for splitting a vector-like object into a List object.
List-utils for common operations on List objects.
Vector objects for the parent class.
The SimpleList class for a direct extension of the List class.
The CompressedList class defined in the IRanges package for another direct extension of the List class.
The IntegerList, RleList, and IRanges classes and constructors defined in the IRanges package for more examples of concrete List subclasses.
The extractList function defined in the IRanges package for grouping elements of a vector-like object into a list-like object.

1	showClass("List") # shows only the known subclasses define in this package

Loading required package: stats4
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Virtual Class "List" [package "S4Vectors"]

Slots:
                                                            
Name:        elementType   elementMetadata          metadata
Class:         character DataFrame_OR_NULL              list

Extends: 
Class "Vector", directly
Class "list_OR_List", directly
Class "Annotated", by class "Vector", distance 2
Class "vector_OR_Vector", by class "Vector", distance 2

Known Subclasses: 
Class "SimpleList", directly
Class "TransposedDataFrame", directly
Class "HitsList", by class "SimpleList", distance 2
Class "DataFrame", by class "SimpleList", distance 2
Class "SelfHitsList", by class "SimpleList", distance 3
Class "SortedByQueryHitsList", by class "SimpleList", distance 3
Class "DFrame", by class "SimpleList", distance 3
Class "SortedByQuerySelfHitsList", by class "SimpleList", distance 4
Class "FilterRules", by class "SimpleList", distance 2