Calculate ROGUE score for Seurat Object — sn_calculate_rogue • Shennong

This function calculates ROGUE score based on Seurat object.

Usage

sn_calculate_rogue(
  x,
  cluster = NULL,
  sample = NULL,
  span = 0.9,
  assay = "RNA",
  layer = "counts"
)

Arguments

x: A Seurat object.
cluster: Column name in metadata specifying cluster labels.
sample: Column name in metadata specifying sample labels.
span: The span parameter for rogue estimation.
assay: Assay used for ROGUE calculation. Defaults to "RNA".
layer: Layer used as the input count matrix. Defaults to "counts".

Value

A data.frame of ROGUE score per cluster/sample or per cluster.

Examples

if (FALSE) { # \dontrun{
data("pbmc_small", package = "Shennong")
pbmc <- sn_run_cluster(pbmc_small, normalization_method = "seurat", verbose = FALSE)
rogue_tbl <- sn_calculate_rogue(pbmc, cluster = "seurat_clusters")
head(rogue_tbl)
} # }