SOMA Read Iterator Over Sparse Matrices

SparseReadIter is a class that allows for iteration over a reads on SOMASparseNDArray.

Super class

tiledbsoma::ReadIter -> SparseReadIter

Methods

Public methods

• SparseReadIter$new()

• SparseReadIter$concat()

• SparseReadIter$clone()

Inherited methods

• tiledbsoma::ReadIter$read_complete()
• tiledbsoma::ReadIter$read_next()

---

Method new()

Create (lifecycle: maturing).

Usage

SparseReadIter$new(sr, shape, zero_based = FALSE)

Arguments

sr

Soma reader pointer.

shape

Shape of the full matrix.

zero_based

Logical, if TRUE will make iterator for Matrix::dgTMatrix-class otherwise matrixZeroBasedView.

---

Method concat()

Concatenate remainder of iterator.

Usage

SparseReadIter$concat()

Returns

matrixZeroBasedView of Matrix::sparseMatrix.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SparseReadIter$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

dir <- withr::local_tempfile(pattern = "matrix-iter")
dir.create(dir, recursive = TRUE)
(exp <- load_dataset("soma-exp-pbmc-small", dir))
#> <SOMAExperiment>
#>   uri: /tmp/RtmpjD0Pq2/matrix-iter270924e7c8c4/soma-exp-pbmc-small
qry <- exp$axis_query("RNA")
xqry <- qry$X("data")

iter <- xqry$sparse_matrix()
stopifnot(inherits(iter, "SparseReadIter"))

while (!iter$read_complete()) {
  block <- iter$read_next()
}