FindAllClusterDE: Run differential expression analysis on every cluster

In WarrenLab/single-cell: Helper Functions For Single-Cell Analysis

Run differential expression analysis on every cluster

Description

Use a given function to perform differential expression analysis between two conditions on every cluster in a Seurat object.

Usage

FindAllClusterDE(seurat, grouping.var, method = RunEdgeR)

Arguments

seurat	A seurat object.
grouping.var	The name of the metadata variable used to group the samples into two groups to compare.
method	A function that takes a seurat object, a cluster number, and a grouping variable, and returns a data.frame with row names as feature names, and the columns p and fold.change. See, for example, RunEdgeR

Value

A data.frame containing one row for each cluster/feature combination, with columns p, fold.change, cluster, and feature.

WarrenLab/single-cell documentation built on June 10, 2022, 1:50 a.m.