Global

Methods

CLONE(x, optionsopt) → {*}

Source:

Clone a vector-like object.

For TypedArrays, this just uses slice(). For Arrays, this creates a copy and runs CLONE on each element in the copy.

Custom classes should provide a _bioconductor_CLONE method to define the cloning operation. This method should accept the same arguments as COMBINE except for x.

Parameters:
Name Type Attributes Default Description
x *

Some vector-like object.
options Object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
deepCopy boolean <optional>
 true

Whether to create a deep copy. The exact interpretation of deepCopy=false is left to each method, but generally speaking, any setter ($-marked) functions operating on the copy should not alter x.
Returns:

A clone of x, i.e., the return value and x should not compare equal. If deepCopy=true, all internal components are also cloned.

Type
*

COMBINE(objects) → {*}

Source:

Combine multiple vector-like objects.

For Array and TypedArrays, the combined array is of a class that avoids information loss.

Custom classes should provide a _bioconductor_COMBINE method to define the combining operation. This method should accept the same arguments as COMBINE.

Parameters:
Name Type Description
objects Array

Array of vector-like objects to be combined. It is assumed that the objects are of the same class, or at least compatible with each other - for custom classes, the definition of "compatibility" depends on the _bioconductor_COMBINE method of the first element of objects.
Returns:

A vector-like object containing the concatenated data from the input objects.

  • If the first entry of objects is an instance of a custom class, the return value should be of the same class.
  • If all objects are TypedArrays of the same class, the return value will be a TypedArray of that class.
  • If any of the objects are Arrays, the return value will be an Array.
  • If any of the objects are 64-bit TypedArrays of different classes, the return value will be an Array.
  • Otherwise, for any other classes of TypedArrays in objects, the return value will be a Float64Array.
Type
*

COMBINE_COLUMNS(objects) → {*}

Source:

Combine multiple two-dimensional objects by column. Custom classes should provide a _bioconductor_COMBINE_COLUMNS method to define the combining operation. This method should accept:

  • an "empty" instance of the class of the first object, to be populated with data.
  • an array of objects to be combined, like objects.
Parameters:
Name Type Description
objects Array

Array of two-dimensional objects to be combined by column. It is assumed that the objects are of the same class, or at least compatible with each other - for custom classes, the definition of "compatibility" depends on the _bioconductor_COMBINE_COLUMNS method of the first element of objects.
Returns:

A two-dimensional object containing the column-wise concatenated data from the input objects, typically of the same class as the first entry of objects.

Type
*

COMBINE_ROWS(objects) → {*}

Source:

Combine multiple two-dimensional objects by row. Custom classes should provide a _bioconductor_COMBINE_ROWS method to define the combining operation. This method should accept:

  • an "empty" instance of the class of the first object, to be populated with data.
  • an array of objects to be combined, like objects.
Parameters:
Name Type Description
objects Array

Array of two-dimensional objects to be combined by row. It is assumed that the objects are of the same class, or at least compatible with each other - for custom classes, the definition of "compatibility" depends on the _bioconductor_COMBINE_ROWS method of the first element of objects.
Returns:

A two-dimensional object containing the row-wise concatenated data from the input objects, typically of the same class as the first entry of objects.

Type
*

flexibleCombineRows(objects) → {DataFrame}

Source:

Flexibly combine multiple DataFrames by row by filling in missing columns with an array of nulls. This is equivalent to calling COMBINE on an array of DataFrames that may have mismatching columns.

Parameters:
Name Type Description
objects Array

Array of DataFrames to be combined.
Returns:

The combined DataFrame, where the number of rows is equal to sum of rows across objects, and the columns is equal to the union of columns across objects.

Type
DataFrame

LENGTH(x) → {number}

Source:

Compute the length of a vector-like object.

For Array and TypedArrays, this just returns the length property directly.

Custom classes should provide a _bioconductor_LENGTH method to describe their length. This method should accept no arguments.

Parameters:
Name Type Description
x *

Some vector-like object.
Returns:

Length of the object.

Type
number

NUMBER_OF_COLUMNS(x) → {number}

Source:

Return the number of columns for a two-dimensional object. Custom classes should provide a _bioconductor_NUMBER_OF_COLUMNS method, accepting no arguments.

Parameters:
Name Type Description
x *

Some two-dimensional object.
Returns:

Number of columns.

Type
number

NUMBER_OF_ROWS(x) → {number}

Source:

Return the number of rows for a two-dimensional object. Custom classes should provide a _bioconductor_NUMBER_OF_ROWS method, accepting no arguments.

Parameters:
Name Type Description
x *

Some two-dimensional object.
Returns:

Number of rows.

Type
number

presplitFactor(factor) → {Object}

Source:

Given a factor, return the indices corresponding to each level. This can be used in subsequent splitRows calls.

Parameters:
Name Type Description
factor Array | TypedArray

Array containing the factor of interest.
Returns:

Object where each key is a factor level and each value is an array containing the indices corresponding to that level in factor.

Type
Object

SLICE(x, i, optionsopt) → {*}

Source:

Slice a vector-like object.

For Array and TypedArrays, this just uses slice() or subarray().

Custom classes should provide a _bioconductor_SLICE method to create a slice. This method should accept the same arguments as SLICE except for x.

Parameters:
Name Type Attributes Default Description
x *

Some vector-like object.
i Object | Array | TypedArray

An Array or TypedArray of integer indices specifying the slice of x to retain.

Alternatively, an object containing start and end, where the slice is defined as the sequence of consecutive integers in [start, end).
options Object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
allowView boolean <optional>
 false

Whether a view can be created to mimic the slice operation. Whether this is actually done depends on the method, but may improve efficiency by avoiding unnecessary copies.
Returns:

A vector-like object, typically of the same class as x, containing data for the specified slice.

If allowInPlace = true, x may be modified in place, and the return value may be a reference to x.

Type
*

SLICE_2D(x, rowsnullable, columnsnullable, optionsopt) → {*}

Source:

Slice a two-dimensional object by its rows and/or columns.

Custom classes should provide a _bioconductor_SLICE_2D method, accepting the same arguments as this generic but with x replaced by an "empty" instance of the same class. Each method should then fill the empty instance with the sliced contents of x.

Parameters:
Name Type Attributes Default Description
x *

Some two-dimensional object.
rows Object | Array | TypedArray <nullable>

An Array or TypedArray of integer indices specifying the row-wise slice of x to retain.

Alternatively, an object containing start and end, where the slice is defined as the sequence of consecutive integers in [start, end).

Alternatively null, to indicate that no slicing is to be performed on the rows.
columns Object | Array | TypedArray <nullable>

An Array or TypedArray of integer indices specifying the column-wise slice of x to retain.

Alternatively, an object containing start and end, where the slice is defined as the sequence of consecutive integers in [start, end).

Alternatively null, to indicate that no slicing is to be performed on the columns.
options Object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
allowView boolean <optional>
 false

Whether a view can be created to mimic the slice operation. Whether this is actually done depends on the method, but may improve efficiency by avoiding unnecessary copies.
Returns:

A two-dimensional object, typically of the same class as x, containing data for the specified slice.

Type
*

SPLIT(x, factor) → {Object}

Source:

Split a vector-like object along its length according to the levels of a factor of the same length. This works automatically for all classes for which there is a SLICE method, but custom classes may also choose to define their own _bioconductor_SPLIT method.

Parameters:
Name Type Description
x *

Some vector-like object.
factor Array | TypedArray

Array containing the factor to use for splitting. This should have the same length as x.

Alternatively, the output of presplitFactor can be supplied.
Returns:

An object containing one key per level of factor, where the value is the slice of x corresponding to the indices of that level in factor.

Type
Object

which(x, optionsopt) → {Array}

Source:
Parameters:
Name Type Attributes Default Description
x Array | TypedArray

Array of values to be interpreted as truthy or falsey.
options Object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
not boolean <optional>
 false

Whether to select the entries of x that are falsey.
Returns:

Array of indices of the entries of x that are truthy (if not=false) or falsey (if not=true). This array is guaranteed to be sorted in ascending order.

Type
Array