import_vdj: Import VDJ data to be added to an SCE object

In friedue/SCEdjvdj: Single-cell VDJ Tools for SCE objects

Description

Import VDJ data to be added to an SCE object

Usage

import_vdj(
  vdj_dir,
  prefix = "",
  cell_prefix = "",
  filter_contigs = TRUE,
  sep = ";"
)

Arguments

vdj_dir	cellranger VDJ output directories. If a vector of multiple paths is provided, an equal number of cell prefixes must also be provided. If a named vector is given, the names will be used to prefix each cell barcode.
prefix	Prefix to add to new colData columns
cell_prefix	Prefix to add to cell barcodes
filter_contigs	Only include chains with at least one productive contig
sep	Separator to use for storing per cell clonotype information in the meta.data
return_SCE	TRUE by default. If set to FALSE, only a data.frame will be returned.

Value

Data.frame with the VDJ info that can be added to the colData of an SCE.

friedue/SCEdjvdj documentation built on April 21, 2021, 7:54 a.m.