getCombinedDataSet-data.frame-Seurat-method: Combine scTCR-seq and scRNA-seq data

In JuanXie19/TCRlineageClust:

Description

This function attatchs the immune receptor information to metadata of the seurat object

Usage

## S4 method for signature 'data.frame,Seurat'
getCombinedDataSet(TCR, seurat, ...)

Arguments

seurat	A seurat object
scTCRseq	The preprocessed scTCR-seq data. See details

Details

The input scTCR-seq needs to be a data frame, and alpha chain and beta chain need to be paired. I If you have multiple sets of scTCR-seq from more than one sample, the data needs to be combined into a single data frame. It should contain a column named 'cell.id' and a cloumn named 'cdr3'. The 'cell.id' column corresponds to the cell barcodes(potentially prefixed with sample name). The 'cdr3' column holds the scTCR-seq information for cells. You are free to provide any related information that can be used to define a clonotype. For instance, you can put CDR3 alpha chain, or beta chain, or paired alpha-beta chain amino acid/nuleotide sequence in this column.

The seurat object must contain clustering results saved as 'clusters', and must have cell barcodes saved as 'cell.id'. #' The barcodes from scTCR-seq data and seurat object must have the same naming style. For instance, if barcodes from seurat/scTCR-seq are prefixed with sample name, then the barcodes from scTCR-seq/seurat must also have prefix.

Value

A object of class CombinedDataSet with clonotype information as well as scRNA-seq information. The assay slot of this object is essentially an updated seurat object, with clonotype information attached.

Examples

TCR <-read.csv("/PATH/TO/YOUR/scTCR-seqData/",header=T)
load('Mice.sub.rda')
getCombinedDataSet(TCR,Mice.sub)

JuanXie19/TCRlineageClust documentation built on Feb. 26, 2022, 12:33 a.m.