ClearGruffi: Remove gruffi results from the Seurat object

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

Remove gruffi results from the Seurat object

Description

Removes corresponding metadata columns and clear @misc$gruffi slot

Usage

ClearGruffi(
  obj,
  pattern.GO.score = "^Score\\.GO\\.[0-9]+",
  pattern.granule.score = ".*_snn_res\\..*\\_cl\\.av_GO\\.[0-9]+",
  stress.assignment = "is.Stressed",
  remove.granules = FALSE
)

Arguments

obj	A Seurat object.
pattern.GO.score	A regex pattern to match GO score columns that should be removed. Default is "^Score\.GO\.0-9+", which matches columns starting with "Score.GO." followed by any number of digits.
pattern.granule.score	A regex pattern to match granule score columns that should be removed. Default is "._snn_res\..\_cl\.av_GO\.0-9+", matching a specific pattern related to granule scores.
stress.assignment	The name of the stress assignment column. Default: "is.Stressed".
remove.granules	Option to also remove the optimal granule resolution. Default: FALSE, because it can take very long time to recompute.

Value

The modified Seurat object with specified columns removed from @meta.data and the @misc$gruffi slot cleared.

Examples

obj <- removeColumnsAndClearGruffi(obj)

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