AssignGranuleAverageScoresFromGOterm: Assign granule average scores from Gene Ontology (GO) terms.

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

Assign granule average scores from Gene Ontology (GO) terms.

Description

Calculates and assigns granule average scores from Gene Ontology (GO) term in a Seurat object. It can compute new GO term scores, plot gene expressions, and save UMAP visualizations. The function updates the Seurat object with cluster average scores for the specified GO term.

Usage

AssignGranuleAverageScoresFromGOterm(
  obj = combined.obj,
  GO_term = "GO:0034976",
  new_GO_term_computation = FALSE,
  clustering = GetGruffiClusteringName(obj),
  save.UMAP = FALSE,
  plot.each.gene = FALSE,
  assay = "RNA",
  description = (if (!is.null(names(GO_term))) names(GO_term) else NULL),
  mirror = NULL,
  stat.av = c("mean", "median", "normalized.mean", "normalized.median")[3],
  overwrite.misc.GO_genes = FALSE,
  ...
)

Arguments

obj	Seurat single cell object, Default: combined.obj
GO_term	The GO term identifier for evaluation, default: 'GO:0034976'.
new_GO_term_computation	Calculate new GO-term score? (or use am existing one?) Default: FALSE
clustering	Which clustering to use (from metadata)? Default: GetGruffiClusteringName(obj) e.g. "integrated_snn_res.48.reassigned"
save.UMAP	Logical indicating whether to save UMAP plots, default: FALSE.
plot.each.gene	Logical indicating whether to plot each gene's expression on UMAP, default: FALSE.
assay	The assay type to use, default: 'RNA'.
description	Description to added to plot title, e.g. GO-terms name, Default: 'NULL'
mirror	Which Ensembl mirror to use in biomaRt::useEnsembl()? If connection to Ensembl fails with default settings, mirror can be specified. Default: 'NULL'
stat.av	How to caluclate the central tendency? Default: c("mean", "median", "normalized.mean", "normalized.median")3
overwrite.misc.GO_genes	Overwrite preexisting gene set in misc$gruffi$GO[[make.names(GO)]].
...	Additional parameters to be passed to the CalculateAndPlotGoTermScores function.

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