SOMASparseNDArrayRead

Intermediate type to choose result format when reading a sparse array

Super class

tiledbsoma::SOMASparseNDArrayReadBase -> SOMASparseNDArrayRead

Methods

Public methods

• SOMASparseNDArrayRead$sparse_matrix()

• SOMASparseNDArrayRead$tables()

• SOMASparseNDArrayRead$blockwise()

Inherited methods

• tiledbsoma::SOMASparseNDArrayReadBase$initialize()

---

Method sparse_matrix()

Read as a sparse matrix (lifecycle: maturing). Returns an iterator of Matrix::dgTMatrix-class or matrixZeroBasedView of it.

Usage

SOMASparseNDArrayRead$sparse_matrix(zero_based = FALSE)

Arguments

zero_based

Logical, if TRUE returns iterator of matrixZeroBasedView if FALSE returns iterator of Matrix::dgTMatrix-class.

Returns

SparseReadIter

---

Method tables()

Read as a arrow::Table (lifecycle: maturing). Returns an iterator of arrow::Table.

Usage

SOMASparseNDArrayRead$tables()

Returns

TableReadIter

---

Method blockwise()

Read in a blockwise fashion

Usage

SOMASparseNDArrayRead$blockwise(
  axis,
  ...,
  size = NULL,
  reindex_disable_on_axis = NA
)

Arguments

axis

Axis to iterate over in a blockwise manner

...

Ignored

size

The size of each blockwise chunk to generate

reindex_disable_on_axis

Additional axes that will not be re-indexed; the following values may be used as shorthands for common settings:

• “TRUE”: disable re-indexing on all axes

• “NA”: re-index only on axis, disable re-indexing on all others

• “FALSE”: re-index on all axes, do not disable re-indexing

Returns

A SOMASparseNDArrayBlockwiseRead iterated reader