as.anndata {scCustomize} | R Documentation |
Convert objects to anndata objects
Description
Convert objects (Seurat & LIGER) to anndata objects
Usage
as.anndata(x, ...)
## S3 method for class 'Seurat'
as.anndata(
x,
file_path,
file_name,
assay = "RNA",
main_layer = "data",
other_layers = "counts",
transer_dimreduc = TRUE,
verbose = TRUE,
...
)
## S3 method for class 'liger'
as.anndata(
x,
file_path,
file_name,
transfer_norm.data = FALSE,
reduction_label = NULL,
add_barcode_names = FALSE,
barcode_prefix = TRUE,
barcode_cell_id_delimiter = "_",
verbose = TRUE,
...
)
Arguments
x |
Seurat or LIGER object |
... |
Arguments passed to other methods |
file_path |
directory file path and/or file name prefix. Defaults to current wd. |
file_name |
file name. |
assay |
Assay containing data to use, (default is "RNA"). |
main_layer |
the layer of data to become default layer in anndata object (default is "data"). |
other_layers |
other data layers to transfer to anndata object (default is "counts"). |
transer_dimreduc |
logical, whether to transfer dimensionality reduction coordinates from Seurat to anndata object (default is TRUE). |
verbose |
logical, whether to print status messages during object conversion (default is TRUE). |
transfer_norm.data |
logical, whether to transfer the norm.data in addition to raw.data, default is FALSE. |
reduction_label |
What to label the visualization dimensionality reduction. LIGER does not store name of technique and therefore needs to be set manually. |
add_barcode_names |
logical, whether to add dataset names to the cell barcodes when merging object data, default is FALSE. |
barcode_prefix |
logical, if |
barcode_cell_id_delimiter |
The delimiter to use when adding dataset id to barcode prefix/suffix. Default is "_". |
Value
an anndata object generated from x
, saved at path provided.
References
Seurat version modified and enhanced version of sceasy::seurat2anndata
(sceasy package: https://github.com/cellgeni/sceasy; License: GPL-3. Function has additional checks and supports Seurat V3 and V5 object structure.
LIGER version inspired by sceasy::seurat2anndata
modified and updated to apply to LIGER objects (sceasy package: https://github.com/cellgeni/sceasy; License: GPL-3.
Examples
## Not run:
as.anndata(x = seurat_object, file_path = "/folder_name", file_name = "anndata_converted.h5ad")
## End(Not run)
## Not run:
as.anndata(x = liger_object, file_path = "/folder_name", file_name = "anndata_converted.h5ad")
## End(Not run)