Add_Alt_Feature_ID: Add Alternative Feature IDs

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

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
)

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).

Value

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

Examples

## Not run: 
# 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")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.