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
names ms_name
Writing Column Pairs
Column-wise relationship matrices are written out as
sparse matrices within the obsp
group
of measurement
names ms_name
Writing Row Pairs
Row-wise relationship matrices are written out as
sparse matrices within the varp
group
of measurement
names 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
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