sce_int_combine_hvgs: Combine HVG data from a list of 'SingleCellExperiment'...

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

Combine HVG data from a list of SingleCellExperiment objects.

Description

This is, in fact, similar to get_top_hvgs(). The only difference is that HVGs are first combined from all SingleCellExperiment objects in sce_list and consequently, top HVGs are selected.

Usage

sce_int_combine_hvgs(
  sce_list,
  hvg_selection_value = 0,
  hvg_metric_fit_name = "hvg_metric_fit",
  hvg_combination = c("hvg_metric", "intersection", "union", "all"),
  hvg_selection = c("top", "significance", "threshold")
)

Arguments

sce_list	A named list of SingleCellExperiment objects.
hvg_selection_value, hvg_selection	See get_top_hvgs().
hvg_metric_fit_name	A character scalar: name of a list item with HVG data in metadata().
hvg_combination	See sce_int_import_fn().

Value

A named list of combined HVG data.

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