FilterStressedCells: Filter Stressed Cells from a Seurat Object

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

Filter Stressed Cells from a Seurat Object

Description

Identifies and filters stressed cells based on specified GO terms and a quantile threshold. It supports optional plotting of exclusion results and saving of modified datasets.

Usage

FilterStressedCells(
  obj = combined.obj,
  res = "integrated_snn_res.30",
  quantile.thr = 0.9,
  GOterms = c(`glycolytic process` = "GO:0006096",
    `response to endoplasmic reticulum stress` = "GO:0034976"),
  direction = "above",
  saveRDS = TRUE,
  saveRDS.Removed = FALSE,
  PlotExclusionByEachScore = TRUE,
  PlotSingleCellExclusion = TRUE,
  GranuleExclusionScatterPlot = TRUE
)

Arguments

obj	Seurat single cell object, Default: combined.obj
res	Clustering resolution, Default: 'integrated_snn_res.30'
quantile.thr	Quantile threshold to cutoff stressed cells, Default: 0.9
GOterms	GO-terms to use for filtering, Default: c(⁠glycolytic process⁠ = "GO:0006096", ⁠response to endoplasmic reticulum stress⁠ = "GO:0034976")
direction	filtering direction, above or below, Default: 'above'
saveRDS	Logical indicating if the filtered object should be saved as an RDS file, default is TRUE.
saveRDS.Removed	Logical indicating if a separate RDS file for removed cells should be saved, default is FALSE.
PlotExclusionByEachScore	Logical for plotting exclusion results by each score, default is TRUE.
PlotSingleCellExclusion	Logical for plotting single cell exclusion results, default is TRUE.
GranuleExclusionScatterPlot	Logical for plotting a scatter plot of granule exclusion, default is TRUE.

See Also

iprint, percentage_formatter calc.cluster.averages filter_HP, llprint reexports

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