RangedSummarizedExperiment

RangedSummarizedExperiment

A RangedSummarizedExperiment is a SummarizedExperiment subclass where each row represents a genomic interval. As such, it stores an additional GRanges or GroupedGRanges of length equal to the number of rows, where each element represents the genomic range(s) for the corresponding row of the SummarizedExperiment.

The RangedSummarizedExperiment supports the same set of generics as the SummarizedExperiment. Each method will call the base method, with the following extensions:

  • SLICE_2D will additionally slice the supplied genomic ranges by the desired rows.
  • COMBINE_ROWS will combine genomic ranges across objects. If some objects contain a GroupedGRanges and other objects contain GRanges, the latter will be coerced to a GroupedGRanges (where each group contains one range) before combining. If any object is a base SummarizedExperiment, a GroupedGRanges containing zero-length groups will be automatically constructed to attempt combining.
  • COMBINE_COLUMNS will use the genomic ranges from the first object.

Constructor

new RangedSummarizedExperiment(assays, rowRangesnullable, optionsopt)

Source:
Parameters:
Name Type Attributes Default Description
assays Object

Object where keys are the assay names and values are multi-dimensional arrays of experimental data. All arrays should have the same number of rows and columns.
rowRanges GRanges | GroupedGRanges <nullable>

Genomic ranges corresponding to each row.

Alternatively, each row may correspond to a group of genomic ranges.

If null, a GroupedGRanges is constructed where each row corresponds to one group of ranges of zero length.
options Object <optional>
 {}

Optional parameters, including those used in the SummarizedExperiment constructor.

Extends

Classes

RangedSummarizedExperiment

Methods

$removeAssay(i) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Description
i string | number

Identity of the assay to add, either by name or index.
Returns:

A reference to this SummarizedExperiment after removing the specified assay.

Type
SummarizedExperiment

$setAssay(i, value) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Description
i string | number

Identity of the assay to add, either by name or index.

  • If i is a number, the assay at the specified index is replaced. i should be non-negative and less than the number of assays.
  • If i is a string, any assay with the same name is replaced. If no such assay exists, a new assay is appended to the list of assays.
value *

Multi-dimensional array-like object to set/add as the assay.
Returns:

A reference to this SummarizedExperiment with modified assays.

Type
SummarizedExperiment

$setAssayNames(names) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Description
names Array

Array of strings containing the assay names. This should be of the same length as the number of assays and contain unique values.
Returns:

A reference to this SummarizedExperiment with modified assay names.

Type
SummarizedExperiment

$setColumnData(value) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Description
value DataFrame

Data frame containing the column annotations. This should have one row for each columns of this SummarizedExperiment.
Returns:

A reference to this SummarizedExperiment with modified column data.

Type
SummarizedExperiment

$setColumnNames(names, optionsopt) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
names Array

Array of strings of length equal to the number of columns in this SummarizedExperiment, containing column names. Alternatively null, to remove all column names.
options Object <optional>
 {}

Optional parameters.

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

Whether to mutate this SummarizedExperiment instance in place. If false, a new instance is returned.
Returns:

The SummarizedExperiment with modified column names. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
SummarizedExperiment

$setMetadata(value) → {Annotated}

Source:
Overrides:
Parameters:
Name Type Description
value Object

Object containing the metadata.
Returns:

A reference to this Annotated object.

Type
Annotated

$setRowData(value) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Description
value DataFrame

Data frame containing the row annotations. This should have one row for each row of this SummarizedExperiment.
Returns:

A reference to this SummarizedExperiment with modified row data.

Type
SummarizedExperiment

$setRowNames(names) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Description
names Array

Array of strings of length equal to the number of rows in this SummarizedExperiment, containing row names. Alternatively null, to remove all row names.
Returns:

A reference to this SummarizedExperiment with modified row names.

Type
SummarizedExperiment

$setRowRanges(value) → {RangedSummarizedExperiment}

Source:
Parameters:
Name Type Description
value GRanges

Genomic ranges corresponding to each row. This should have length equal to the number of rows in this RangedSummarizedExperiment.
Returns:

A reference to this RangedSummarizedExperiment after modifying its rowRanges.

Type
RangedSummarizedExperiment

$sliceAssays(i) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Description
i Array

Array of strings or indices specifying the assays to retain in the slice. This should refer to unique assay names.
Returns:

A reference to this SummarizedExperiment with sliced assays.

Type
SummarizedExperiment

assay(i) → {*}

Source:
Overrides:
Parameters:
Name Type Description
i string | number

Assay to retrieve, either by name or index.
Returns:

The contents of assay i as an multi-dimensional array-like object.

Type
*

assayNames() → {Array}

Source:
Overrides:
Returns:

Array of assay names.

Type
Array

columnData() → {DataFrame}

Source:
Overrides:
Returns:

Data frame of column data, with one row per column in this SummarizedExperiment.

Type
DataFrame

columnNames() → (nullable) {Array}

Source:
Overrides:
Returns:

Array of strings containing column names, or null if no column names are available.

Type
Array

metadata() → {Map}

Source:
Overrides:
Returns:

Map containing arbitrary metadata.

Type
Map

numberOfAssays() → {number}

Source:
Overrides:
Returns:

Number of assays.

Type
number

numberOfColumns() → {number}

Source:
Overrides:
Returns:

Number of columns in this SummarizedExperiment.

Type
number

numberOfRows() → {number}

Source:
Overrides:
Returns:

Number of rows in this SummarizedExperiment.

Type
number

removeAssay(i, optionsopt) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
i string | number

Identity of the assay to add, either by name or index.
options Object <optional>
 {}

Optional parameters.

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

Whether to mutate this SummarizedExperiment instance in place. If false, a new instance is returned.
Returns:

The SummarizedExperiment after removing the specified assay. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
SummarizedExperiment

rowData() → {DataFrame}

Source:
Overrides:
Returns:

Data frame of row data, with one row per row in this SummarizedExperiment.

Type
DataFrame

rowNames() → (nullable) {Array}

Source:
Overrides:
Returns:

Array of strings containing row names, or null if no row names are available.

Type
Array

rowRanges() → {GRanges}

Source:
Returns:

Genomic ranges corresponding to each row.

Type
GRanges

setAssay(i, value, optionsopt) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
i string | number

Identity of the assay to add, either by name or index.

  • If i is a number, the assay at the specified index is replaced. i should be non-negative and less than the number of assays.
  • If i is a string, any assay with the same name is replaced. If no such assay exists, a new assay is appended to the list of assays.
value *

Multi-dimensional array-like object to set/add as the assay.
options Object <optional>
 {}

Optional parameters.

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

Whether to mutate this SummarizedExperiment instance in place. If false, a new instance is returned.
Returns:

A SummarizedExperiment with modified assays. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
SummarizedExperiment

setAssayNames(names, optionsopt) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
names Array

Array of strings containing the assay names. This should be of the same length as the number of assays and contain unique values.
options Object <optional>
 {}

Optional parameters.

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

Whether to mutate this SummarizedExperiment instance in place. If false, a new instance is returned.
Returns:

The SummarizedExperiment with modified assay names. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
SummarizedExperiment

setColumnData(value, optionsopt) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
value DataFrame

Data frame containing the column annotations. This should have one row for each columns of this SummarizedExperiment.
options Object <optional>
 {}

Optional parameters.

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

Whether to mutate this SummarizedExperiment instance in place. If false, a new instance is returned.
Returns:

The SummarizedExperiment with modified column data. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
SummarizedExperiment

setColumnNames(names, optionsopt) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
names Array

Array of strings of length equal to the number of columns in this SummarizedExperiment, containing column names. Alternatively null, to remove all column names.
options Object <optional>
 {}

Optional parameters.

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

Whether to mutate this SummarizedExperiment instance in place. If false, a new instance is returned.
Returns:

The SummarizedExperiment with modified column names. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
SummarizedExperiment

setMetadata(value, optionsopt) → {Annotated}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
value Object | Map

Object containing the metadata.
options Object <optional>
 {}

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

setRowData(value, optionsopt) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
value DataFrame

Data frame containing the row annotations. This should have one row for each row of this SummarizedExperiment.
options Object <optional>
 {}

Optional parameters.

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

Whether to mutate this SummarizedExperiment instance in place. If false, a new instance is returned.
Returns:

The SummarizedExperiment with modified row data. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
SummarizedExperiment

setRowNames(names, optionsopt) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
names Array

Array of strings of length equal to the number of rows in this SummarizedExperiment, containing row names. Alternatively null, to remove all row names.
options Object <optional>
 {}

Optional parameters.

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

Whether to mutate this SummarizedExperiment instance in place. If false, a new instance is returned.
Returns:

The SummarizedExperiment with modified row names. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
SummarizedExperiment

setRowRanges(value, optionsopt) → {RangedSummarizedExperiment}

Source:
Parameters:
Name Type Attributes Default Description
value GRanges

Genomic ranges corresponding to each row. This should have length equal to the number of rows in this RangedSummarizedExperiment.
options Object <optional>
 {}

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 RangedSummarizedExperiment after modifying its rowRanges. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
RangedSummarizedExperiment

sliceAssays(i, optionsopt) → {SummarizedExperiment}

Source:
Overrides:
Parameters:
Name Type Attributes Default Description
i Array

Array of strings or indices specifying the assays to retain in the slice. This should refer to unique assay names.
options Object <optional>
 {}

Optional parameters.

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

Whether to mutate this SummarizedExperiment instance in place. If false, a new instance is returned.
Returns:

The SummarizedExperiment with sliced assays. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type
SummarizedExperiment