scCustomize (version 3.0.1)

Add_Alt_Feature_ID: Add Alternative Feature IDs

Description

Add alternative feature ids data.frame to the misc slot of Seurat object.

Usage

Add_Alt_Feature_ID(
  seurat_object,
  features_tsv_file = NULL,
  hdf5_file = NULL,
  assay = NULL,
  data_name = "feature_id_mapping_table",
  overwrite = FALSE
)

Value

Seurat Object with new entries in the obj@misc slot.

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.

data_name

name to use for data.frame when stored in @misc slot.

overwrite

logical, whether to overwrite item with the same data_name in the @misc slot of object (default is FALSE).

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")
}