addTCR: addTCR
In Artur-man/VDJChef: VDJChef for vdj analysis

addTCR

R Documentation

addTCR

Description

This functions adds a TCR contig metadata to existing Seurat or ExpressionSet object.

Usage

addTCR(exsc, tcrmeta)

Arguments

`exsc`	SatijaLab’s Seurat Class or Bioconductor’s ExpressionSet Class
`tcrmeta`	TCR clonotype metadata with rownames as barcodes (i.e. output of function "getTCR"). Barcodes must match that of @param exsc

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

Seurat Object or ExpressionSet with metadata updated with TCR clonotypes

Examples

# library
library(Seurat)
library(Biobase)

# Read h5 data and create a Seurat object
seu.data <- Read10X_h5(filename = system.file("extdata", "sc5p_v2_hs_T_1k_multi_5gex_t_count_filtered_feature_bc_matrix.h5", package="VDJChef"))
seu <- CreateSeuratObject(counts=seu.data)
meta <- seu@meta.data
meta$barcode <- rownames(meta)

# Create an ExpressionSet object
eset <- ExpressionSet(as.matrix(seu@assays$RNA@counts))
pData(eset) <- seu@meta.data

# import TCR metadata
tcrmeta <- getTCR(system.file("extdata", "1kcells-multi/vdj_t/", package="VDJChef"))
seu <- addTCR(seu, tcrmeta)
eset <- addTCR(eset, tcrmeta)

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