Add alternative feature ids to the assay level meta.data slot in Assay5 compatible object (Seurat V5.0.0 or greater)
Add_Alt_Feature_ID(
seurat_object,
features_tsv_file = NULL,
hdf5_file = NULL,
assay = NULL
)
object name.
output file from Cell Ranger used for creation of Seurat object.
(Either provide this of hdf5_file
)
output file from Cell Ranger used for creation of Seurat object.
(Either provide this of features_tsv_file
)
name of assay(s) to add the alternative features to. Can specify "all" to add to all assays.
Seurat Object with new entries in the obj@assays$ASSAY@meta.data
slot.
if (FALSE) {
# Using features.tsv.gz file
# Either file from filtered or raw outputs can be used as they are identical.
obj <- Add_Alt_Feature_ID(seurat_object = obj,
features_tsv = "sample01/outs/filtered_feature_bc_matrix/features.tsv.gz", assay = "RNA")
#' # Using hdf5 file
# Either filtered_feature_bc or raw_feature_bc can be used as the features slot is identical
# Though it is faster to load filtered_feature_bc file due to droplet filtering
obj <- Add_Alt_Feature_ID(seurat_object = obj,
hdf5_file = "sample01/outs/outs/filtered_feature_bc_matrix.h5", assay = "RNA")
}