sce_remove_cc_genes: Remove cell cycle-related genes from HVGs.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Remove cell cycle-related genes from HVGs.

Description

Remove cell cycle-related genes from HVGs.

Usage

sce_remove_cc_genes(
  sce,
  var_expl_threshold,
  variable = "phase",
  hvg_metric_fit = NULL,
  ...
)

Arguments

sce	A SingleCellExperiment object.
var_expl_threshold	A numeric scalar: threshold for variance explained. Genes exceeding this threshold will be marked as CC-related.
variable	A character scalar: column to use for variance explained computation.
hvg_metric_fit	A DataFrame object.
...	Passed to get_top_hvgs().

Value

A SingleCellExperiment object with removed CC-related genes from HVGs.

is_cc_related logical column is appended to rowData(sce).

The following items of metadata(sce) are added or modified:

• hvg_cc_genes_var_expl_threshold: the value of var_expl_threshold.

• hvg_ids: if CC-related genes are found, their IDs are removed.

• hvg_rm_cc_genes_ids: IDs of CC-related genes. If these are not found, an empty vector.

Note that CC-related genes are not removed from metadata(sce)$hvg_metric_fit.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.