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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
)

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 names 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