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Write a SummarizedExperiment object to a SOMA

Source: R/write_bioc.R
write_soma.SummarizedExperiment.Rd

Write a SummarizedExperiment object to a SOMA

Usage

# S3 method for class 'SummarizedExperiment'
write_soma(
  x,
  uri,
  ms_name,
  ...,
  ingest_mode = "write",
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  context = NULL
)

Arguments

x

An object.

uri

URI for resulting SOMA object.

ms_name

Name for resulting measurement.

...

Arguments passed to other methods

ingest_mode

Ingestion mode when creating the SOMA; choose from:

  • “write”: create a new SOMA and error if it already exists.

  • “resume”: attempt to create a new SOMA; if it already exists, simply open it for writing.

platform_config

Optional platform configuration.

tiledbsoma_ctx

Optional (DEPRECATED) SOMATileDBContext.

context

Optional SOMAContext object used for TileDB operations. If a context is not provided, then the default context will be used. Call set_default_context once before other SOMA operations to configure the default context.

Value

The URI to the resulting SOMAExperiment generated from the data contained in x.

Writing colData

colData is written out as a data frame called “obs” at the experiment level.

Writing Assay Matrices

Each assay matrix is written out as a sparse matrix within the X group of measurement named ms_name. Names for assay matrices within X are taken from the assay names. Assay matrices are transposed (samples as rows) prior to writing.

Writing rowData

rowData is written out as a data frame called “var” at the measurement level.

Examples

if (FALSE) { # requireNamespace("withr", quietly = TRUE) && requireNamespace("SummarizedExperiment", quietly = TRUE)
# \donttest{
uri <- withr::local_tempfile(pattern = "summarized-experiment")

mat <- abs(Matrix::rsparsematrix(
  230L,
  80L,
  0.3,
  dimnames = list(paste0("feature_", seq_len(230)), paste0("cell_", seq_len(80)))
))
(se <- SummarizedExperiment::SummarizedExperiment(list(counts = mat, logcounts = log2(mat + 1L))))

uri <- write_soma(se, uri, ms_name = "RNA")

(exp <- SOMAExperimentOpen(uri))
exp$obs
(ms <- exp$ms$get("RNA"))
ms$var
ms$X$names()

exp$close()
# }
}