Single-cell Annotation Matrix

Single-cell Annotation Matrix

Single-cell Annotation Matrix

Details

Base class for matrix-like data with rows aligned to the observations or features of a SOMA.

Super classes

tiledbsc::TileDBObject -> tiledbsc::TileDBArray -> tiledbsc::AnnotationArray -> AnnotationMatrix

Public fields

verbose

Print status messages

Methods

Public methods

• AnnotationMatrix$from_matrix()

• AnnotationMatrix$to_matrix()

• AnnotationMatrix$clone()

Inherited methods

• tiledbsc::TileDBObject$class()
• tiledbsc::TileDBObject$exists()
• tiledbsc::TileDBArray$add_metadata()
• tiledbsc::TileDBArray$array_exists()
• tiledbsc::TileDBArray$attributes()
• tiledbsc::TileDBArray$attrnames()
• tiledbsc::TileDBArray$dimensions()
• tiledbsc::TileDBArray$dimnames()
• tiledbsc::TileDBArray$fragment_count()
• tiledbsc::TileDBArray$get_metadata()
• tiledbsc::TileDBArray$initialize()
• tiledbsc::TileDBArray$print()
• tiledbsc::TileDBArray$reset_query()
• tiledbsc::TileDBArray$schema()
• tiledbsc::TileDBArray$set_query()
• tiledbsc::TileDBArray$tiledb_array()

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Method from_matrix()

Ingest annotation matrix

Usage

AnnotationMatrix$from_matrix(x, index_col)

Arguments

x

any matrix-like object coercible to a TsparseMatrix with string dimensions.

index_col

Name to use for the TileDB array's dimension that will contain the matrix row names.

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Method to_matrix()

Retrieve the annotation data from TileDB

Usage

AnnotationMatrix$to_matrix(attrs = NULL, batch_mode = FALSE)

Arguments

attrs

A character vector of the attribute names to retrieve. By default, all attributes are retrieved.

batch_mode

logical, if TRUE, batch query mode is enabled, which provides the ability to detect partial query results and resubmit until all results are retrieved.

Returns

A matrix

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Method clone()

The objects of this class are cloneable with this method.

Usage

AnnotationMatrix$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.