Write a SingleCellExperiment object to a SOMA
Source: R/write_bioc.R
write_soma.SingleCellExperiment.RdWrite a SingleCellExperiment
object to a SOMA
Usage
# S3 method for SingleCellExperiment
write_soma(
x,
uri,
ms_name = NULL,
...,
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
- 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