SOMA Read Iterator Over Arrow Tables

TableReadIter is a class that allows for iteration over a reads on SOMASparseNDArray and SOMADataFrame. Iteration chunks are retrieved as an Arrow Table.

Super class

tiledbsoma::ReadIter -> TableReadIter

Methods

Public methods

• TableReadIter$concat()

• TableReadIter$clone()

Inherited methods

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

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Method concat()

Concatenate remainder of iterator.

Usage

TableReadIter$concat()

Returns

An Arrow Table.

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Method clone()

The objects of this class are cloneable with this method.

Usage

TableReadIter$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

dir <- withr::local_tempfile(pattern = "table-iter")
dir.create(dir, recursive = TRUE)
(exp <- load_dataset("soma-exp-pbmc-small", dir))
#> <SOMAExperiment>
#>   uri: /tmp/RtmpjD0Pq2/table-iter27093f11957b/soma-exp-pbmc-small
qry <- exp$axis_query("RNA")
xqry <- qry$X("data")

iter <- xqry$tables()
stopifnot(inherits(iter, "TableReadIter"))

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