PerformDifferentialExpression: PerformDifferentialExpression

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

PerformDifferentialExpression

Description

This is designed to perform DE using edgeR on a pseudobulked seurat object

Usage

PerformDifferentialExpression(
  fit,
  contrast,
  contrast_name,
  logFC_threshold = 1,
  FDR_threshold = 0.05,
  test.use = "QLF",
  showPlots = T
)

Arguments

fit	The glm fit object generated by PerformGlmFit
contrast	The contrast, passed directly to edgeR::glmQLFTest or edgeR::glmLRT
contrast_name	A name for the contrast
logFC_threshold	The min logFC
FDR_threshold	The min FDR to report
test.use	Can be either QLF or LRT. QLF runs edgeR::glmQLFTest, while LRT runs edgeR::glmLRT
showPlots	Boolean determining if the volcano plots and p value dsitributions should be shown.

Value

A list with the differential_expression results, volcano ggplot object and pvalue_dist ggplot object

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.