seurat_vdj_add_to_meta: Add VDJ info to Seurat object

In Terkild/scvdj:

Add VDJ info to Seurat object

Description

Adds parsed contig by cell dataframe into metadata of a Seurat object

Usage

seurat_vdj_add_to_meta(
  object,
  VDJ,
  column.CB = "CB",
  prefix = "VDJ_",
  columns.include = c("clonotype.1", "clonotype.2", "clonotype.other", "CDR3.1",
    "CDR3.2", "CDR3.other", "V.1", "V.2", "V.other", "D.1", "D.2", "D.other", "J.1",
    "J.2", "J.other", "C.1", "C.2", "C.other", "UMIcount.1", "UMIcount.2",
    "UMIcount.other", "reads.1", "reads.2", "reads.other"),
  chains = NULL,
  create.boolean = TRUE,
  boolean.suffix = ".bool",
  boolean.filterFunctional = FALSE
)

Arguments

object	Seurat object
VDJ	Parsed VDJ contig by cell data.frame
column.CB	Name of column that contains cell barcode
prefix	Prefix given to each metadata column
chains	Vector of chains (TRA, TRB, TRG, TRD, IGH, IHK, IGL) to include from parsed contig by cell data.frame
create.boolean	Should a boolean of whether a given cell has any expression of a given chain be included
boolean.suffix	Suffix for boolean (default structure is CHAIN.bool)
boolean.filterFunctional	Should boolean only consider "functional" VDJ counts
colums.include	Columns from parsed contig by cell data.frame to be included in Seurat metadata

Value

Seurat object

Terkild/scvdj documentation built on Oct. 22, 2023, 11:12 p.m.