Write a SummarizedExperiment object to a SOMA

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
)

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 SOMATileDBContext.

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()
# }
}