combined_pbmc: Example Multi-sampled T-cell seurat object with integrated...

In APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles

Example Multi-sampled T-cell seurat object with integrated TCR library

Description

Generated with scRepertoire::combineExpression. To construct this object from scratch, try:

scRepertoire::combineExpression(scRepertoire::combineTCR(get(data("contig_list", , package = "scRepertoire")), samples = c("P17B", "P17L", "P18B", , "P18L", "P19B", "P19L", "P20B", "P20L"), removeNA = FALSE, , removeMulti = FALSE, filterMulti = FALSE), get(data("scRep_example", , package = "scRepertoire")), cloneCall = "gene", proportion = TRUE)

Usage

data("combined_pbmc")

Format

A Seurat object with the following slots filled

assays

Currently only contains one assay ("RNA" - scRNA-seq expression data)

• counts - Raw expression data

• data - Normalized expression data

• scale.data - Scaled expression data

• var.features - names of the current features selected as variable

• meta.features - Assay level metadata such as mean and variance

meta.data

Cell level metadata with a combined TCR contig list ⁠from scRepertoire⁠

active.assay

Current default assay

active.ident

Current default idents

graphs

Neighbor graphs computed, currently stores the SNN

reductions

Dimensional reductions: UMAP

version

Seurat version used to create the object

commands

Command history, including the one used to create this object "combineExpression"

APackOfTheClones documentation built on Oct. 11, 2024, 1:08 a.m.