calculate_pseudo_bulk: Calculate pseudo-bulk RNA-Seq data from scRNA-Seq.

In altairwei/rhapsodykit: A Set of Tools for BD Rhapsody WTA Downstream Analysis

Calculate pseudo-bulk RNA-Seq data from scRNA-Seq.

Description

Calculate pseudo-bulk RNA-Seq data from scRNA-Seq.

Usage

calculate_pseudo_bulk(
  sce,
  type = c("counts", "logcounts", "cpm", "vstresiduals"),
  fun = NULL,
  ...
)

Arguments

sce	A SingleCellExperiment object. The following cell metadata (colData) columns have to be provided: sample_id unique sample identifiers cluster_id subpopulation (cluster) assignments group_id experimental group/condition
type	Value type of pseudo-bulk data.
fun	Function used to calculate pseudobulk, mean or sum. If fun is not specified, it will be chosen according type
...	Args passed to muscat::aggregateData

Value

A SingleCellExperiment object.

altairwei/rhapsodykit documentation built on Feb. 1, 2023, 8:52 a.m.