Add Alternative Feature IDs

Source: R/Object_Utilities.R

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
)

Arguments

seurat_object

object name.

features_tsv_file

output file from Cell Ranger used for creation of Seurat object. (Either provide this of hdf5_file)

hdf5_file

output file from Cell Ranger used for creation of Seurat object. (Either provide this of features_tsv_file)

assay

name of assay(s) to add the alternative features to. Can specify "all" to add to all assays.

Value

Seurat Object with new entries in the obj@assays$ASSAY@meta.data slot.

Examples

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")
}