Vector-class: Vector objects

In AdamLeckenby/S4Vectors_Fix: S4 implementation of vector-like and list-like objects

Description

The Vector virtual class serves as the heart of the S4Vectors package and has over 90 subclasses. It serves a similar role as vector in base R.

The Vector class supports the storage of global and element-wise metadata:

1. The global metadata annotates the object as a whole: this metadata is accessed via the metadata accessor and is represented as an ordinary list;

2. The element-wise metadata annotates individual elements of the object: this metadata is accessed via the mcols accessor (mcols stands for metadata columns) and is represented as a DataTable object (i.e. as an instance of a concrete subclass of DataTable, e.g. a DataFrame object), with a row for each element and a column for each metadata variable. Note that the element-wise metadata can also be NULL.

To be functional, a class that inherits from Vector must define at least a length and a "[" method.

Accessors

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

length(x): Get the number of elements in x.

lengths(x, use.names=TRUE): Get the length of each of the elements.

Note: The lengths method for Vector objects is currently defined as an alias for elementNROWS (with addition of the use.names argument), so is equivalent to sapply(x, NROW), not to sapply(x, length). See ?BiocGenerics::lengths in the BiocGenerics package for more information about this.

NROW(x): Defined as length(x) for any Vector object that is not a DataTable object. If x is a DataTable object, then it's defined as nrow(x).

names(x), names(x) <- value: Get or set the names of the elements in the Vector.

rename(x, value, ...): Replace the names of x according to a mapping defined by a named character vector, formed by concatenating value with any arguments in .... The names of the character vector indicate the source names, and the corresponding values the destination names. This also works on a plain old vector.

nlevels(x): Returns the number of factor levels.

mcols(x, use.names=FALSE), mcols(x) <- value: Get or set the metadata columns. If use.names=TRUE and the metadata columns are not NULL, then the names of x are propagated as the row names of the returned DataTable object. When setting the metadata columns, the supplied value must be NULL or a DataTable object holding element-wise metadata.

elementMetadata(x, use.names=FALSE), elementMetadata(x) <- value, values(x, use.names=FALSE), values(x) <- value: Alternatives to mcols functions. Their use is discouraged.

Coercion

as(from, "data.frame"), as.data.frame(from): Coerces from, a Vector, to a data.frame by first coercing the Vector to a vector via as.vector. Note that many Vector derivatives do not support as.vector, so this coercion is possible only for certain types.

as.env(x): Constructs an environment object containing the elements of mcols(x).

Subsetting

In the code snippets below, x is a Vector object or regular R vector object. The R vector object methods for window are defined in this package and the remaining methods are defined in base R.

x[i, drop=TRUE]: If defined, returns a new Vector object made of selected elements i, which can be missing; an NA-free logical, numeric, or character vector; or a logical Rle object. The drop argument specifies whether or not to coerce the returned sequence to an ordinary vector.

x[i] <- value: Replacement version of x[i].

Combining

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

c(x, ...): Combine x and the Vector objects in ... together. Any object in ... must belong to the same class as x, or to one of its subclasses, or must be NULL. The result is an object of the same class as x.

append(x, values, after = length(x)): Insert the Vector values onto x at the position given by after. values must have an elementType that extends that of x.

expand.grid(...): Find cartesian product of every vector in ... and return a data.frame, each column of which corresponds to an argument. See expand.grid.

Displaying

[FOR ADVANCED USERS OR DEVELOPERS]

Displaying of a Vector object is controlled by 2 internal helpers, classNameForDisplay and showAsCell.

For most objects classNameForDisplay(x) just returns class(x). However, for some objects it can return the name of a parent class that is more suitable for display because it's simpler and as informative as the real class name. See SimpleList objects (defined in this package) and CompressedList objects (defined in the IRanges package) for examples of objects for which classNameForDisplay returns the name of a parent class.

showAsCell(x) produces a character vector parallel to x (i.e. with one string per vector element in x) that contains compact string representations of each elements in x.

Note that classNameForDisplay and showAsCell are generic functions so developers can implement methods to control how their own Vector extension gets displayed.

See Also

• Rle, Hits, IRanges and XRaw for example implementations.

• Vector-comparison for comparing, ordering, and tabulating vector-like objects.

• Vector-setops for set operations on vector-like objects.

• Vector-merge for merging vector-like objects.

• List for a direct Vector extension that serves a similar role as list in base R.

• extractList for grouping elements of a vector-like object into a list-like object.

• DataTable which is the type of objects returned by the mcols accessor.

• The Annotated class, which Vector extends.

Examples

showClass("Vector")  # shows (some of) the known subclasses

AdamLeckenby/S4Vectors_Fix documentation built on May 23, 2019, 2:42 p.m.