getCombinedDataSet: Initialize an object of class 'CombinedDataSet'

In JuanXie19/LRT: LRT (Lineage estimation by integrative analysis of single-cell RNA-seq and TCR-seq data)

Initialize an object of class CombinedDataSet

Description

Construct a CombinedDataSet object with Seurat clustering results and clonotype information . Additional helper methods for manipulating CombinedDatSet objects are also described below.

Usage

getCombinedDataSet(TCR, seurat, ...)

Arguments

seurat	An integrated Seurat object. The object must contain clustering results and saved as 'clusters', and must have cell barcodes saved as 'cell.id'
scTCRseq	The preprocessed scTCR-seq data. See details

Details

The input scTCR-seq needs to be a dataframe, and alpha chain and beta chain need to be paired. If you have multiple sets of scTCR-seq from more than one sample, the data needs to be combined into one.

The seurat object must contain clustering results and saved as 'clusters', contain cell barcodes saved as 'cell.id' and also need to have UMAP coordinates for cells.

JuanXie19/LRT documentation built on April 14, 2025, 7:09 p.m.