Add Odd-barcode–derived metadata to a Seurat object

sciT datasets often consist of cells from different treatment conditions. Using Odd barcodes embedded in the full cell barcode, cells can be stratified by treatment or condition. This function extracts the Odd barcode from the full barcode stored in the Seurat metadata, matches it to a user-provided metadata table, and adds both the Odd barcode and the corresponding condition as new metadata columns to the Seurat object contained within an lseurat object.

Usage

Add_odd_barcode_metadata(
  lseurat,
  Odd_barcode_md_file,
  full_barcode_col = "BC",
  condition_col = "condition",
  Odd_barcode_col = "Odd_barcode",
  Odd_barcode_position = 2
)

Arguments

lseurat

An object of class lseurat containing a Seurat object in lseurat$seurat.

Odd_barcode_md_file

A comma-separated file linking Odd barcode IDs to metadata (e.g. treatment or condition). Must contain at least two columns: one with Odd barcode identifiers and one with the corresponding condition.

full_barcode_col

Character string specifying the column name in the Seurat metadata that contains the full cell barcode. Defaults to "BC".

condition_col

Character string specifying the name of the metadata column to store the condition labels in the Seurat object. Defaults to "condition".

Odd_barcode_col

Character string specifying the name of the metadata column to store the extracted Odd barcodes in the Seurat object. Defaults to "Odd_barcode".

Odd_barcode_position

Integer specifying the position of the Odd barcode after splitting the full barcode on underscores ("_"). Defaults to 2.

Value

The input lseurat object with updated Seurat metadata. Two new columns are added to lseurat$seurat@meta.data: one containing the extracted Odd barcodes and one containing the corresponding condition labels.

Details

The full barcode is split using underscores, and the element at Odd_barcode_position is interpreted as the Odd barcode. These Odd barcodes are then matched to the metadata file using exact matching.