CustomScoreEvaluation: CustomScoreEvaluation

In jn-goe/gruffi: Gruffi identifies and removes stressed cells from brain organoid single-cell datasets.

CustomScoreEvaluation

Description

Custom gene-set derived score evaluation for filtering.

Usage

CustomScoreEvaluation(
  obj = combined.obj,
  custom.score.name = "Score.heGENES",
  clustering = GetGruffiClusteringName(obj),
  assay = "RNA",
  stat.av = c("mean", "median", "normalized.mean", "normalized.median")[3],
  ...
)

Arguments

obj	Seurat single cell object, Default: combined.obj
custom.score.name	Name of your custom gene set.
clustering	Which clustering to use (from metadata)? Default: GetGruffiClusteringName(obj) e.g. "integrated_snn_res.48.reassigned"
assay	Which assay to use?, Default: 'RNA'
stat.av	How to caluclate the central tendency? Default: c("mean", "median", "normalized.mean", "normalized.median")3

See Also

reexports iprint

jn-goe/gruffi documentation built on Nov. 7, 2024, 10:38 p.m.