SeuratAddVariants: Add the variant information contained in a genotype object to...

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

Add the variant information contained in a genotype object to a Seurat object

Description

The genotype object should contain a consensus call (vartrix conventions), reference allele count, alternate allele count, and a frequency matrix (typically offset by one to distinguish 0 frequency from no data in an efficient sparse matrix format), as well as metadata about the variants. By default, the single cell matrices will be stored in assays named VAR, REF, ALT and FREQ respectively, and the metadata will be added to the VAR assay feature metadata.

Usage

SeuratAddVariants(
  seurat,
  genotype,
  consensus = "VAR",
  reference = "REF",
  alternate = "ALT",
  frequency = "FREQ"
)

Arguments

seurat	Seurat object.
genotype	Genotype object.
consensus	character(1). The name of the Seurat assay that will store the consensus matrix (values 0 = no data, 1 = ref/ref, 2=alt/alt, 3=ref/alt).
reference	character(1). The name of the Seurat assay that will store the reference allele count matrix.
alternate	character(1). The name of the Seurat assay that will store the alternate allele count matrix.
frequency	character(1). The name of the Seurat assay that will store the frequency matrix (0 = no data, 1-2 = ref only to alt only).

Examples

# MySeuratObject <- SeuratAddVariants(MySeuratObject, MyGenotypeObject)

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