GroupedGRanges - Documentation

Constructor

new GroupedGRanges(ranges, optionsopt)

Source:

GroupedGRanges.js, line 25

Parameters:

Name Type Attributes Default Description

ranges

Array | GRanges

An array of GRanges objects, where each element represents a group of genomic ranges. All objects should have compatible columns in their elementMetadata.

Alternatively, a single GRanges containing a concatenation of ranges from all groups. In this case, rangeLengths must be supplied.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`rangeLengths`	TypedArray \| Array	<optional> <nullable>	`null`	Length of the ranges within each group. This should be coercible to an Int32Array, contain non-negative values, and have a sum equal to the length of `ranges`. Only used if `ranges` is a single GRanges object, where each group's ranges are assumed to form contiguous intervals along `ranges`.
`names`	Array	<optional> <nullable>	`null`	Array of strings of length equal to `start`, containing names for each genomic range. Alternatively `null`, in which case the ranges are assumed to be unnamed.
`elementMetadata`	DataFrame	<optional> <nullable>	`null`	A DataFrame with number of rows equal to the length of `start`, containing arbitrary per-range annotations. Alternatively `null`, in which case a zero-column DataFrame is automatically constructed.
`metadata`	Object \| Array \| Map \| List	<optional>	`{}`	Arbitrary metadata, see the Annotated constructor.

Extends

Vector

Classes

GroupedGRanges

Methods

(static) empty(numberOfGroupsopt) → {GroupedGRanges}

Source:

GroupedGRanges.js, line 369

Parameters:

Name	Type	Attributes	Default	Description
`numberOfGroups`	number	<optional>	`0`	Numbe of empty groups to create.

Returns:

A GroupedGRanges object of length equal to numberOfGroups, where each group is of zero length.

Type: GroupedGRanges

buildOverlapIndex(optionsopt) → {GroupedGRangesOverlapIndex}

Source:

GroupedGRanges.js, line 277

Parameters:

Name Type Attributes Default Description

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`restrictToSeqnames`	Array \| Set	<optional> <nullable>	`null`	Array or Set containing the sequence names to use in the index. If `null`, all available sequence names are used.
`restrictToStrand`	Array \| Set	<optional> <nullable>	`null`	Array or Set containing the strands to use in the index. If `null`, all available strands are used.

Returns:

A pre-built index for computing overlaps with other GRanges instances.

Type: GroupedGRangesOverlapIndex

elementMetadata() → {DataFrame}

Source:

Vector.js, line 61

Overrides:

Vector#elementMetadata

Returns:

A DataFrame with one row corresponding to each vector element, containing arbitrary per-element metadata.

Type: DataFrame

group(i, optionsopt) → {GRanges}

Source:

GroupedGRanges.js, line 129

Parameters:

Name Type Attributes Default Description

i

number

Index of the group of interest.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`allowView`	boolean	<optional>	`false`	Whether a view can be created in any internal slicing operations.

Returns:

The genomic ranges for group i.

Type: GRanges

metadata() → {List}

Source:

Annotated.js, line 36

Overrides:

Vector#metadata

Returns:

List of arbitrary metadata.

Type: List

names() → (nullable) {Array}

Source:

Vector.js, line 68

Overrides:

Vector#names

Returns:

Array of strings containing the name of each range, or null if no names are available.

Type: Array

numberOfGroups() → {number}

Source:

GroupedGRanges.js, line 138

Returns:

Number of groups in this object.

Type: number

rangeLengths() → {Int32Array}

Source:

GroupedGRanges.js, line 117

Returns:

The length of each group's ranges along the concatenated set of ranges returned by ranges.

Type: Int32Array

ranges() → {GRanges}

Source:

GroupedGRanges.js, line 101

Returns:

The concatenated set of ranges across all groups.

Type: GRanges

rangeStarts() → {Int32Array}

Source:

GroupedGRanges.js, line 109

Returns:

The start indices for each group's ranges along the concatenated set of ranges returned by ranges.

Type: Int32Array

setElementMetadata(elementMetadatanullable, optionsopt) → {Vector}

Source:

Vector.js, line 87

Overrides:

Vector#setElementMetadata

Parameters:

Name Type Attributes Default Description

elementMetadata

DataFrame

Arbitrary metadata for each vector element. This should have number of rows equal to the vector length. Alternatively null, in which case all existing per-element metadata is removed.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this Vector instance in place. If `false`, a new instance is returned.

Returns:

The Vector object after setting the element metadata to value. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: Vector

setGroup(i, ranges, optionsopt) → {GroupedGRanges}

Source:

GroupedGRanges.js, line 242

Multiple consecutive calls to $setGroup are not executed immediately. Rather, the operations are staged and executed in batch once the modified GroupedGRanges is used in other methods. This enables efficient setting of individual groups inside a single concatenated GRanges.

Parameters:

Name Type Attributes Default Description

i

number

Index of the group of interest.

ranges

GRanges

Genomic ranges for group i.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this GroupedGRanges instance in place. If `false`, a new instance is returned.

Returns:

The GroupedGRanges object after setting group i. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: GroupedGRanges

setMetadata(value, optionsopt) → {Annotated}

Source:

Annotated.js, line 53

Overrides:

Vector#setMetadata

Parameters:

Name Type Attributes Default Description

value

Object | Map | Array | List

Object containing the metadata.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this Annotated instance in place. If `false`, a new instance is returned.

Returns:

The Annotated object after replacing the metadata. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: Annotated

setNames(namesnullable, optionsopt) → {Vector}

Source:

Vector.js, line 108

Overrides:

Vector#setNames

Parameters:

Name Type Attributes Default Description

names

Array

Array of strings containing a name for each range. This should have length equal to the number of ranges. Alternatively null, if no names are present.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this Vector instance in place. If `false`, a new instance is returned.

Returns:

The Vector object after setting the names to value. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: Vector

setRanges(ranges, optionsopt) → {GroupedGRanges}

Source:

GroupedGRanges.js, line 155

Parameters:

Name Type Attributes Default Description

ranges

GRanges

Genomic ranges of length equal to the concatenated set of ranges returned by ranges.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this GroupedGRanges instance in place. If `false`, a new instance is returned.

Returns:

The GroupedGRanges object after modifying the internal ranges. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: GroupedGRanges