CellSimilarityToGenotypes: Compute the similarity of single cells in a Seurat object to...

In nbroguiere/burgertools: Collection of tools extending the functionality of Seurat

Compute the similarity of single cells in a Seurat object to the reference genotypes in a genotype object

Description

Computes the fraction of matching variants between single cells in a Seurat object and the reference genotypes in a genotype object. Store this similarity measure in a new assay within the Seurat object.

Usage

CellSimilarityToGenotypes(
  seurat,
  genotype,
  assay.name = "similarity",
  prefix = "Similarity-",
  features.use = "all",
  assays = c("VAR", "REF", "ALT"),
  layers = c("data", "data", "data")
)

Arguments

seurat	A seurat object
genotype	A genotype object
assay.name	character(1). The name under which the similarities are stored in the seurat object (Default: "similarity").
prefix	character(1). A prefix appended to the genotype names to generate the feature names in the similarity assay (Default: "Similarity-").
features.use	character(n). The features (i.e. variants) to be used for the similarity calculations. Can be a vector of variants by name, or NA to use informative variants if available, or "all" (Default: "all").
assays	character(3). The name of the assays within the Seurat object that contain the variant calls (sparse matrix with values 1,2,3 in vartrix conventions), and counts of reference and alt alleles (Default: c("VAR","REF","ALT")).
layers	The layers to use within the assays above (Default: c("data","data","data")).

Details

The similarity is defined as the fraction of variants which have an identical call (i.e. ref/ref, alt/alt, or ref/alt) in individual cells compared to the reference genotype. Variants which are not covered by any read at the single cell level are ignored and do not contribute to the similarity value. Variants which are covered by only one read are always considered a match with a heterozygous reference genotype.

Value

Returns the Seurat object

Examples

MySeuratObject <- CellSimilarityToGenotypes(MySeuratObject,MyGenotypes)
DefaultAssay(MySeuratObject) <- "similarity"
FeaturePlot(MySeuratObject,"Similarity-MyGenotypeName1")

nbroguiere/burgertools documentation built on Jan. 30, 2024, 3:48 a.m.