get_snp_counts — get_snp_counts • scatools

Computes per feature counts across the dataset. Equivalent to pseudobulk summarization.

Usage

get_snp_counts(sce, variables = "all", target_assays = c("ref", "alt"))

Arguments

sce: SingleCellExperiment object with one or more assays
variables: Factors upon which to split the counts. Defaults to 'all' which counts across entire dataset
target_assays: Assays in sce to count

Value

A SingleCellExperiment object with named counts for each assay in the rowData(sce) slot.

Examples

if (FALSE) { # \dontrun{
sce <- get_snp_counts(sce,
  variables = c("all", "Sample", "Condition"),
  target_assays = c("ref", "alt")
)
} # }