pseudobulk_diff_state: Perform differential state analysis on pseudo-bulk data.

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

Perform differential state analysis on pseudo-bulk data.

Description

Perform differential state analysis on pseudo-bulk data.

Usage

pseudobulk_diff_state(
  sce,
  pb,
  contrasts = NULL,
  method = c("edgeR", "DESeq2", "limma-trend", "limma-voom"),
  ...
)

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
pb	Object return by calculate_pseudo_bulk
contrasts	Character vector specifying contrasts, see makeContrasts. If NULL, all possible combination will be tested.
method	Specify which bulk RNA-seq DE methods to apply.
...	pass to pbDS

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