getTCR: getTCR

In Artur-man/VDJChef: VDJChef for vdj analysis

getTCR

Description

Imports a contig and clonotype (if exists) metadata from Cell Ranger VDJ output directory.

Usage

getTCR(vdj_dir, filteredcontigs = TRUE, removeNA = FALSE, removeMulti = FALSE)

Arguments

vdj_dir	Path to 10X Genomics Cellranger vdj (or multi) output of VDJ contigs
removeNA	Remove any chain with without values
removeMulti	Remove barcodes with more than 2 chains
contigfile	Contig info (10X Genomics VDJ output: filtered_contig_annotations.csv or all_filtered_contig_annotations.csv)
clonotypefile	Clonotype metadata info(10X Genomics VDJ output: clonotypes.csv)
filterMulti	This option will allow for the selection of the 2 corresponding chains with the highest expression for a single barcode.

Details

Reads output directory of Cellranger VDJ (or multi) to output clonotype metadata (TCR chains, VDJ genes, reads, umis). If extra info on T cell metadata is available (clonotypes.csv), it will be joined to the clonotype metadata.

Example dataset:
https://www.10xgenomics.com/resources/datasets/human-t-cells-from-a-healthy-donor-1-k-cells-multi-v-2-2-standard-5-0-0
https://www.10xgenomics.com/resources/datasets/human-pbmc-from-a-healthy-donor-10-k-cells-multi-v-2-2-standard-5-0-0

Value

Data frame of clonotypes for individual cell barcodes

Examples

# Import TCR metadata
tcrmeta <- getTCR(system.file("extdata", "1kcells-multi/vdj_t/", package="VDJChef"))
tcrmeta <- getTCR(system.file("extdata", "1kcells-multi/vdj_t/", package="VDJChef"), filteredcontigs = FALSE, removeMulti = TRUE)

Artur-man/VDJChef documentation built on Oct. 2, 2022, 9 p.m.