SOMA Blockwise Read Iterator for Arrow Tables

Class that allows for blockwise read iteration of SOMA reads as Arrow Tables.

Super classes

tiledbsoma::ReadIter -> tiledbsoma::BlockwiseReadIterBase -> BlockwiseTableReadIter

Methods

Public methods

• BlockwiseTableReadIter$concat()

• BlockwiseTableReadIter$clone()

Inherited methods

• tiledbsoma::BlockwiseReadIterBase$initialize()
• tiledbsoma::BlockwiseReadIterBase$read_complete()
• tiledbsoma::BlockwiseReadIterBase$read_next()

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Method concat()

Concatenate the remainder of the blockwise iterator.

Usage

BlockwiseTableReadIter$concat()

Returns

An Arrow Table with the remainder of the iterator.

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Method clone()

The objects of this class are cloneable with this method.

Usage

BlockwiseTableReadIter$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

dir <- withr::local_tempfile(pattern = "blockwise-table")
dir.create(dir, recursive = TRUE)
(exp <- load_dataset("soma-exp-pbmc-small", dir))
#> <SOMAExperiment>
#>   uri: /tmp/RtmpgbdEWv/blockwise-table276a2dc237f/soma-exp-pbmc-small
qry <- exp$axis_query("RNA")
xqry <- qry$X("data")

iter <- xqry$blockwise(0L, size = 20L, reindex_disable_on_axis = TRUE)$tables()
stopifnot(inherits(iter, "BlockwiseTableReadIter"))

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