GRanges - Documentation

Constructor

new GRanges(seqnames, ranges, optionsopt)

Source:

GRanges.js, line 21

Parameters:

Name Type Attributes Default Description

seqnames

Array

Array of strings containing the sequence names for each genomic range.

ranges

IRanges

Position and width of the range on its specified sequence. This should have the same length as seqnames.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`strand`	Array \| TypedArray	<optional> <nullable>	`null`	Array containing the strandedness of each genomic range. This should be 0 (any strand), 1 (forward strand) or -1 (reverse strand). If `null`, this is assumed to be 0 for all genomic 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	<optional>	`{}`	Object containing arbitrary metadata as key-value pairs.

Extends

Vector

Classes

GRanges

Methods

(static) empty() → {GRanges}

Source:

GRanges.js, line 321

Returns:

A zero-length GRanges object.

Type: GRanges

$setElementMetadata(elementMetadatanullable) → {Vector}

Source:

Vector.js, line 98

Overrides:

Vector#$setElementMetadata

Parameters:

Name	Type	Attributes	Description
`elementMetadata`	DataFrame	<nullable>	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.

Returns:

A reference to this Vector object after setting the element metadata to value.

Type: Vector

$setMetadata(value) → {Annotated}

Source:

Annotated.js, line 55

Overrides:

Vector#$setMetadata

Parameters:

Name	Type	Description
`value`	Object	Object containing the metadata.

Returns:

A reference to this Annotated object.

Type: Annotated

$setNames(namesnullable) → {Vector}

Source:

Vector.js, line 129

Overrides:

Vector#$setNames

Parameters:

Name	Type	Attributes	Description
`names`	Array	<nullable>	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.

Returns:

A reference to this Vector object after setting the element metadata to value.

Type: Vector

$setRanges(ranges) → {GRanges}

Source:

GRanges.js, line 185

Parameters:

Name	Type	Description
`ranges`	IRanges	Start positions and widths for each genomic range. This should have length equal to the number of ranges.

Returns:

A reference to this GRanges object after setting the ranges to ranges.

Type: GRanges

$setSeqnames(seqnames) → {GRanges}

Source:

GRanges.js, line 152

Parameters:

Name	Type	Description
`seqnames`	Array	Array of strings containing the sequence names for each genomic range.

Returns:

A reference to this GRanges object after setting the sequence names to seqnames.

Type: GRanges

$setStrand(strand) → {GRanges}

Source:

GRanges.js, line 219

Parameters:

Name	Type	Description
`strand`	Array \| TypedArray	Array of strands for each genomic range. This should have length equal to the number of ranges. Entries may be 0 (any strand), 1 (forward strand) or -1 (reverse strand).

Returns:

A reference to this GRanges object after setting the strands to strand.

Type: GRanges

buildOverlapIndex(optionsopt) → {GRangesOverlapIndex}

Source:

GRanges.js, line 236

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: GRangesOverlapIndex

elementMetadata() → {DataFrame}

Source:

Vector.js, line 59

Overrides:

Vector#elementMetadata

Returns:

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

Type: DataFrame

end() → {Int32Array}

Source:

GRanges.js, line 96

Returns:

Array of integers containing the end position (specifically, one-past-the-end) for each genomic range.

Type: Int32Array

metadata() → {Map}

Source:

Annotated.js, line 28

Overrides:

Vector#metadata

Returns:

Map containing arbitrary metadata.

Type: Map

names() → (nullable) {Array}

Source:

Vector.js, line 66

Overrides:

Vector#names

Returns:

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

Type: Array

ranges() → {IRanges}

Source:

GRanges.js, line 117

Returns:

Start positions and widths for all ranges on their specified sequence names.

Type: IRanges

seqnames() → {Array}

Source:

GRanges.js, line 110

Returns:

Array of strings containing the sequence name for each genomic range.

Type: Array

setElementMetadata(elementMetadatanullable, optionsopt) → {Vector}

Source:

Vector.js, line 85

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

setMetadata(value, optionsopt) → {Annotated}

Source:

Annotated.js, line 45

Overrides:

Vector#setMetadata

Parameters:

Name Type Attributes Default Description

value

Object | Map

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 113

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) → {GRanges}

Source:

GRanges.js, line 166

Parameters:

Name Type Attributes Default Description

ranges

IRanges

Start positions and widths for each genomic range. This should have length equal to the number of ranges.

options

Object

{}

Optional parameters.

Properties

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

Returns:

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

Type: GRanges

setSeqnames(seqnames, optionsopt) → {GRanges}

Source:

GRanges.js, line 141

Parameters:

Name Type Attributes Default Description

seqnames

Array

Array of strings containing the sequence names for each genomic range.

options

Object

{}

Optional parameters.

Properties

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

Returns:

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

Type: GRanges

setStrand(strand, optionsopt) → {GRanges}

Source:

GRanges.js, line 200

Parameters:

Name Type Attributes Default Description

strand

Array | TypedArray

Array of strands for each genomic range. This should have length equal to the number of ranges. Entries may be 0 (any strand), 1 (forward strand) or -1 (reverse strand).

options

Object

{}

Optional parameters.

Properties

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

Returns:

The GRanges object after setting the strands to strand. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: GRanges

start() → {Int32Array}

Source:

GRanges.js, line 89

Returns:

Array of integers containing the start position for each genomic range.

Type: Int32Array

strand() → {Int8Array}

Source:

GRanges.js, line 124

Returns:

Array containing the strandedness for each genomic range - 0 (any strand), 1 (forward strand) or -1 (reverse strand).

Type: Int8Array

width() → {Int32Array}

Source:

GRanges.js, line 103

Returns:

Array of integers containing the width of each genomic range.

Type: Int32Array