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Write a SingleCellExperiment object to a SOMA

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

Write a SingleCellExperiment object to a SOMA

Usage

# S3 method for class 'SingleCellExperiment'
write_soma(
  x,
  uri,
  ms_name = NULL,
  ...,
  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; defaults to mainExpName(x).

...

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 Reduced Dimensions

Reduced dimensions are written out as sparse matrices within the obsm group of measurement named ms_name.

Writing Column Pairs

Column-wise relationship matrices are written out as sparse matrices within the obsp group of measurement named ms_name.

Writing Row Pairs

Row-wise relationship matrices are written out as sparse matrices within the varp group of measurement named ms_name.

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("SingleCellExperiment", quietly = TRUE)
# \donttest{
uri <- withr::local_tempfile(pattern = "single-cell-experiment")

mat <- abs(Matrix::rsparsematrix(
  230L,
  80L,
  0.3,
  dimnames = list(paste0("feature_", seq_len(230)), paste0("cell_", seq_len(80)))
))
(sce <- SingleCellExperiment::SingleCellExperiment(
  assays = list(counts = mat, logcounts = log2(mat + 1L)),
  reducedDims = list(
    pca = matrix(stats::runif(80 * 5L), nrow = 80),
    tsne = matrix(stats::rnorm(80 * 2L), nrow = 80)
  ),
  mainExpName = "RNA"
))

uri <- write_soma(sce, uri)

(exp <- SOMAExperimentOpen(uri))
exp$close()
# }
}