Example Multi-sampled T-cell seurat object with integrated TCR library
Source:R/data.R
combined_pbmc.Rd![[Stable]](figures/lifecycle-stable.svg)
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
-
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"