Generate DEGs based on OAR score

Usage

oar_deg(
  data,
  seurat_v5 = T,
  score = NULL,
  count.filter = 1,
  splines = TRUE,
  degrees.freedom = 5,
  blacklisted.genes = NULL,
  auto.threshold = TRUE,
  custom.tr = NULL,
  score.name = "OARscore"
)

Arguments

data: a Seurat (v5) object or a data.frame with cell barcodes as column names and genes as row names. Seurat object must have a column in metadata with OARscore.
seurat_v5: a boolean to indicate if supplied data is a Seurat object, default is TRUE. If FALSE, user must supply a score vector.
score: a named numeric vector with OARscores to be used in the model. Names should be cell barcodes. Ignored if Seurat object is supplied.
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.
splines: a boolean to indicate if splines should be used to fit model, default is TRUE
degrees.freedom: a numeric value indicating the degrees of freedom to calculate splines. Default is 5. Values between 3 and 5 are recommended.
blacklisted.genes: a character vector with gene names to be excluded from the analysis. Default is empty.
auto.threshold: a boolean to indicate if FDR threshold should be calculated from the data, default is TRUE
custom.tr: a numeric value to use as an FDR threshold. Ignored if auto.threshold is set to TRUE.
score.name: name of OAR score in dataset, default is "OARscore". If suffix used on previous functions, would need to include full new name here.

Value

A data.frame with p-values for genes that significantly contribute to OAR score.

Examples

if (FALSE) { # \dontrun{
degs <- oar_deg(data)
} # }