Single line pipeline to run complete analysis

Usage

oar(
  data,
  seurat_v5 = TRUE,
  count.filter = 1,
  blacklisted.genes = NULL,
  suffix = "",
  cores = 1,
  store.hamming = TRUE
)

data: a Seurat (v5) object or a matrix with cell barcodes as column names and genes as row names.
seurat_v5: a boolean to indicate if supplied data is a Seurat object, default is TRUE
count.filter: a numeric value indicating the minimum fraction of cells expressing any given gene that will be included in the analysis, default is 1. Values between 0.5 and 2 are recommended.
blacklisted.genes: a character vector with gene names to be excluded from the analysis. Default is empty.
suffix: a string to append to the output variables. Default is empty
cores: a numeric value indicating the number of cores to use un parallel processing. Use parallel::detectCores() or parallelly::availableCores() to identify possibilities. Default is 1.
store.hamming: a boolean to control if hamming distances should be stored in the Seurat object. Default set to TRUE

A Seurat object with OAR stats added into meta data, or a matrix with OAR stats.

if (FALSE) { # \dontrun{
pbmcs <- oar(pbmcs)
} # }