add_seurat_metadata: Define 10x clonotypes

In victoraLab/clonality: Easily Define Groups Of T/B Cells

Define 10x clonotypes

Description

Takes a list of paired chains and defines clonotypes.

Usage

add_seurat_metadata(
  seu = NULL,
  clonal.list = ls(pattern = "^Clonal", envir = .GlobalEnv),
  cdr3_map = "cdr3_col2",
  cell = "T",
  purity = 0.8,
  stick_only = "all",
  sticky = FALSE,
  overwrite = T
)

Arguments

seu	Seurat. A seurat object to embed with clonality data.
clonal.list	Character. The clonalities to be inserted into the seurat metadata. Default: ls(pattern = "^Clonal").
cdr3_map	Character. The columun name to be used to map single chains to paired chains. CDR3 for nt ; cdr3_col2 for aa. Default: "cdr3_col2".
cell	Character. Possible values: B Bcells, T Tcells, Tgd Tcells GamaDelta.
purity	Numeric. Minimum fraction of the dominant mapped paired to be used in a sticky assignment.
stick_only	Character vector. Possible values: TRA, TRB, TRD, TRG, IGH, IGK, IGL, all. Default: all
sticky	Logical. If the script should merge the clonality of single chain cells with paired cells.
overwrite	Logical. Whether to overwrite clonality columns from seurat.

victoraLab/clonality documentation built on March 19, 2024, 7:41 p.m.