R/getCombinedDataSet.r

In JuanXie19/TCRlineageClust:

#' Combine scTCR-seq and scRNA-seq data 
#'
#' This function attatchs the immune receptor information to metadata of the seurat object
#' @param scTCRseq The preprocessed scTCR-seq data. See details
#' @param seurat A seurat object
#'
#' @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.
#'
#' @details 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.
#'
#' @import Seurat
#' @import dplyr
#'
#' @export
#'
#' @return A object of class \code{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)
#'
setMethod(f='getCombinedDataSet',
		signature = signature(TCR='data.frame',seurat='Seurat'),
		definition = function(TCR,seurat,...){
			TCR <- subset(TCR, barcode %in% seurat$cell.id)
			TCR$cdr3 <-TCR$cdr3_aa2
			CHECK <- identical(TCR$barcode,names(seurat$cell.id))
			if(CHECK==0) stop('barcode from scTCR-seq and scRNA-seq not match, please check! ')
			TCR <- TCR[order(match(TCR$barcode,seurat$cell.id)),]   # reorder the TCR dataframe to make sure we assign correct cdr3 to the seurat object
			seurat$cdr3 <- TCR$cdr3
			CombinedData <-new('CombinedDataSet',seurat = seurat)
			return(CombinedData)
		}

)