RunEdgeR: Run edgeR to perform DE analysis

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

Run edgeR to perform DE analysis

Description

Run edgeR to assign a p-value to each feature for the null hypothesis that this feature is not significantly differently expressed between the cells of a given cluster between the two levels of a condition. This gives edgeR raw counts, and uses cellular detection rate as a covariate. Based on https://github.com/csoneson/conquer_comparison/blob/master/scripts/apply_edgeRQLFDetRate.R

Usage

RunEdgeR(seurat, cluster, grouping.var)

Arguments

seurat	A seurat object.
cluster	The number of a cluster to perform DE analysis on
grouping.var	The name of the metadata variable used to group the samples into two groups to compare.

Value

A data.frame with row names as feature names, and the columns p and fold.change.

Examples

de.results <- RunEdgeR(seurat, 0, 'challenge_status')

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